Mercurial > repos > galaxyp > openms_filefilter
annotate FileFilter.xml @ 16:86a9dd43dd09 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:44:21 +0000 |
| parents | fe4e4587d265 |
| children |
| rev | line source |
|---|---|
|
7
fce0d752c6c5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
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changeset
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1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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2 <!--Proposed Tool Section: [File Filtering / Extraction / Merging]--> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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3 <tool id="FileFilter" name="FileFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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changeset
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4 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files</description> |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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changeset
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5 <macros> |
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fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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changeset
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6 <token name="@EXECUTABLE@">FileFilter</token> |
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fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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changeset
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7 <import>macros.xml</import> |
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fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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changeset
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8 </macros> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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9 <expand macro="requirements"/> |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
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10 <expand macro="stdio"/> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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12 @EXT_FOO@ |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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13 #import re |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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14 |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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changeset
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15 ## Preprocessing |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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16 mkdir in && |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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18 mkdir out && |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
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19 #if $spectra.blackorwhitelist.file: |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
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20 mkdir spectra.blackorwhitelist.file && |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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21 cp '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' && |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
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22 #end if |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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23 #if $consensus.blackorwhitelist.file: |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
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changeset
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24 mkdir consensus.blackorwhitelist.file && |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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25 cp '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' && |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
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26 #end if |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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changeset
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27 #if $id.blacklist: |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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28 mkdir id.blacklist && |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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29 cp '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' && |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
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30 #end if |
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fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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31 |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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32 ## Main program call |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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33 |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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34 set -o pipefail && |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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35 @EXECUTABLE@ -write_ctd ./ && |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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38 -in |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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40 -out |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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41 'out/output.${out_type}' |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
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42 #if $spectra.blackorwhitelist.file: |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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43 -spectra:blackorwhitelist:file |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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44 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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45 #end if |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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46 #if $consensus.blackorwhitelist.file: |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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47 -consensus:blackorwhitelist:file |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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48 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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49 #end if |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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50 #if $id.blacklist: |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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51 -id:blacklist |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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52 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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53 #end if |
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fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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54 |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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55 ## Postprocessing |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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56 && mv 'out/output.${out_type}' '$out' |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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57 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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58 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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59 #end if]]></command> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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60 <configfiles> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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61 <inputs name="args_json" data_style="paths"/> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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63 </configfiles> |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
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64 <inputs> |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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65 <param argument="-in" type="data" format="consensusxml,featurexml,mzml" label="Input file" help=" select consensusxml,featurexml,mzml data sets(s)"/> |
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86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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66 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help=""> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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67 <option value="consensusXML">consensusxml</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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68 <option value="featureXML">featurexml</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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69 <option value="mzML">mzml</option> |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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70 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator> |
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15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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71 <expand macro="list_string_san" name="out_type"/> |
|
0
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72 </param> |
|
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73 <param argument="-rt" type="text" value=":" label="Retention time range to extract" help=""> |
|
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74 <expand macro="list_string_san" name="rt"/> |
|
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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75 </param> |
|
16
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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76 <param argument="-mz" type="text" value=":" label="m/z range to extract (applies to ALL ms levels!)" help=""> |
|
15
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77 <expand macro="list_string_san" name="mz"/> |
|
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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78 </param> |
|
16
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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79 <param argument="-int" type="text" value=":" label="Intensity range to extract" help=""> |
|
15
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80 <expand macro="list_string_san" name="int"/> |
|
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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81 </param> |
|
15
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82 <param argument="-sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the output according to RT and m/z" help=""/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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83 <section name="peak_options" title="Peak data options" help="" expanded="false"> |
|
16
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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84 <param name="sn" argument="-peak_options:sn" type="float" value="0.0" label="Write peaks with S/N > 'sn' values only" help=""/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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85 <param name="rm_pc_charge" argument="-peak_options:rm_pc_charge" type="text" optional="true" value="" label="Remove MS(2) spectra with these precursor charges" help="All spectra without precursor are kept! (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
|
15
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86 <expand macro="list_integer_valsan" name="rm_pc_charge"/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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87 </param> |
|
16
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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88 <param name="pc_mz_range" argument="-peak_options:pc_mz_range" type="text" value=":" label="MSn (n>=2) precursor filtering according to their m/z value" help="Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag"> |
|
15
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89 <expand macro="list_string_san" name="pc_mz_range"/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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90 </param> |
|
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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91 <param name="pc_mz_list" argument="-peak_options:pc_mz_list" type="text" optional="true" value="" label="List of m/z values" help="If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
|
15
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92 <expand macro="list_float_valsan" name="pc_mz_list"/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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93 </param> |
|
16
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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94 <param name="level" argument="-peak_options:level" type="text" value="1 2 3" label="MS levels to extract" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
|
15
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95 <expand macro="list_integer_valsan" name="level"/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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96 </param> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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97 <param name="sort_peaks" argument="-peak_options:sort_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the peaks according to m/z" help=""/> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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98 <param name="no_chromatograms" argument="-peak_options:no_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No conversion to space-saving real chromatograms" help="e.g. from SRM scans"/> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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99 <param name="remove_chromatograms" argument="-peak_options:remove_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes chromatograms stored in a file" help=""/> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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100 <param name="remove_empty" argument="-peak_options:remove_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes spectra and chromatograms without peaks" help=""/> |
|
16
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101 <param name="mz_precision" argument="-peak_options:mz_precision" type="select" label="Store base64 encoded m/z data using 32 or 64 bit precision" help=""> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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102 <option value="32">32</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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103 <option value="64" selected="true">64</option> |
|
15
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104 <expand macro="list_string_san" name="mz_precision"/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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105 </param> |
|
16
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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106 <param name="int_precision" argument="-peak_options:int_precision" type="select" label="Store base64 encoded intensity data using 32 or 64 bit precision" help=""> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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107 <option value="32" selected="true">32</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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108 <option value="64">64</option> |
|
15
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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109 <expand macro="list_string_san" name="int_precision"/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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110 </param> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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111 <param name="indexed_file" argument="-peak_options:indexed_file" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to add an index to the file when writing" help=""/> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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112 <param name="zlib_compression" argument="-peak_options:zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to store data with zlib compression (lossless compression)" help=""/> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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113 <section name="numpress" title="Numpress compression for peak data" help="" expanded="false"> |
|
16
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114 <param name="masstime" argument="-peak_options:numpress:masstime" type="select" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help=""> |
|
11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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115 <option value="none" selected="true">none</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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116 <option value="linear">linear</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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117 <option value="pic">pic</option> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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118 <option value="slof">slof</option> |
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15
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119 <expand macro="list_string_san" name="masstime"/> |
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11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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120 </param> |
|
16
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121 <param name="lossy_mass_accuracy" argument="-peak_options:numpress:lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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122 <param name="intensity" argument="-peak_options:numpress:intensity" type="select" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help=""> |
|
11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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123 <option value="none" selected="true">none</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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124 <option value="linear">linear</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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125 <option value="pic">pic</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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126 <option value="slof">slof</option> |
|
15
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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127 <expand macro="list_string_san" name="intensity"/> |
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11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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128 </param> |
|
16
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129 <param name="float_da" argument="-peak_options:numpress:float_da" type="select" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help=""> |
|
11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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130 <option value="none" selected="true">none</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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131 <option value="linear">linear</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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132 <option value="pic">pic</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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133 <option value="slof">slof</option> |
|
15
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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134 <expand macro="list_string_san" name="float_da"/> |
|
11
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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135 </param> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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136 </section> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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137 </section> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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138 <section name="spectra" title="Remove spectra or select spectra (removing all others) with certain properties" help="" expanded="false"> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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139 <param name="remove_zoom" argument="-spectra:remove_zoom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove zoom (enhanced resolution) scans" help=""/> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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140 <param name="remove_mode" argument="-spectra:remove_mode" type="select" optional="true" label="Remove scans by scan mode" help=""> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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141 <option value="Unknown">Unknown</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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142 <option value="MassSpectrum">MassSpectrum</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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143 <option value="MS1Spectrum">MS1Spectrum</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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144 <option value="MSnSpectrum">MSnSpectrum</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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145 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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146 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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147 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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148 <option value="ConstantNeutralGain">ConstantNeutralGain</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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149 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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150 <option value="Precursor">Precursor</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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151 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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152 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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153 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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154 <option value="Emission">Emission</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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155 <option value="Absorption">Absorption</option> |
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15
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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156 <expand macro="list_string_san" name="remove_mode"/> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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157 </param> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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158 <param name="remove_activation" argument="-spectra:remove_activation" type="select" optional="true" label="Remove MSn scans where any of its precursors features a certain activation method" help=""> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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159 <option value="Collision-induced dissociation">Collision-induced dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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160 <option value="Post-source decay">Post-source decay</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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161 <option value="Plasma desorption">Plasma desorption</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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162 <option value="Surface-induced dissociation">Surface-induced dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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163 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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164 <option value="Electron capture dissociation">Electron capture dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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165 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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166 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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167 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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168 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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169 <option value="Photodissociation">Photodissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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170 <option value="Electron transfer dissociation">Electron transfer dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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171 <option value="Pulsed q dissociation">Pulsed q dissociation</option> |
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15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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172 <option value="trap-type collision-induced dissociation">trap-type collision-induced dissociation</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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173 <option value="beam-type collision-induced dissociation">beam-type collision-induced dissociation</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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174 <option value="in-source collision-induced dissociation">in-source collision-induced dissociation</option> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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175 <option value="Bruker proprietary method">Bruker proprietary method</option> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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176 <expand macro="list_string_san" name="remove_activation"/> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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177 </param> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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178 <param name="remove_collision_energy" argument="-spectra:remove_collision_energy" type="text" value=":" label="Remove MSn scans with a collision energy in the given interval" help=""> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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179 <expand macro="list_string_san" name="remove_collision_energy"/> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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180 </param> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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181 <param name="remove_isolation_window_width" argument="-spectra:remove_isolation_window_width" type="text" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help=""> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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182 <expand macro="list_string_san" name="remove_isolation_window_width"/> |
|
11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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183 </param> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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184 <param name="select_zoom" argument="-spectra:select_zoom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Select zoom (enhanced resolution) scans" help=""/> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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185 <param name="select_mode" argument="-spectra:select_mode" type="select" optional="true" label="Selects scans by scan mode." help=""> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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186 <option value="Unknown">Unknown</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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187 <option value="MassSpectrum">MassSpectrum</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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188 <option value="MS1Spectrum">MS1Spectrum</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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189 <option value="MSnSpectrum">MSnSpectrum</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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190 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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191 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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192 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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193 <option value="ConstantNeutralGain">ConstantNeutralGain</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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194 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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195 <option value="Precursor">Precursor</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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196 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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197 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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198 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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199 <option value="Emission">Emission</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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200 <option value="Absorption">Absorption</option> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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201 <expand macro="list_string_san" name="select_mode"/> |
|
11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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202 </param> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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203 <param name="select_activation" argument="-spectra:select_activation" type="select" optional="true" label="Retain MSn scans where any of its precursors features a certain activation method" help=""> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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204 <option value="Collision-induced dissociation">Collision-induced dissociation</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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205 <option value="Post-source decay">Post-source decay</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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206 <option value="Plasma desorption">Plasma desorption</option> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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207 <option value="Surface-induced dissociation">Surface-induced dissociation</option> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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208 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> |
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209 <option value="Electron capture dissociation">Electron capture dissociation</option> |
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210 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> |
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211 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> |
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212 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> |
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213 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> |
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214 <option value="Photodissociation">Photodissociation</option> |
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215 <option value="Electron transfer dissociation">Electron transfer dissociation</option> |
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216 <option value="Pulsed q dissociation">Pulsed q dissociation</option> |
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217 <option value="trap-type collision-induced dissociation">trap-type collision-induced dissociation</option> |
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218 <option value="beam-type collision-induced dissociation">beam-type collision-induced dissociation</option> |
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219 <option value="in-source collision-induced dissociation">in-source collision-induced dissociation</option> |
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220 <option value="Bruker proprietary method">Bruker proprietary method</option> |
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221 <expand macro="list_string_san" name="select_activation"/> |
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222 </param> |
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223 <param name="select_collision_energy" argument="-spectra:select_collision_energy" type="text" value=":" label="Select MSn scans with a collision energy in the given interval" help=""> |
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224 <expand macro="list_string_san" name="select_collision_energy"/> |
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225 </param> |
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226 <param name="select_isolation_window_width" argument="-spectra:select_isolation_window_width" type="text" value=":" label="Select MSn scans whose isolation window width is in the given interval" help=""> |
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227 <expand macro="list_string_san" name="select_isolation_window_width"/> |
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228 </param> |
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229 <param name="select_polarity" argument="-spectra:select_polarity" type="select" optional="true" label="Retain MSn scans with a certain scan polarity" help=""> |
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230 <option value="unknown">unknown</option> |
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231 <option value="positive">positive</option> |
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232 <option value="negative">negative</option> |
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233 <expand macro="list_string_san" name="select_polarity"/> |
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234 </param> |
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235 <param name="replace_pc_charge" argument="-spectra:replace_pc_charge" type="text" value=":" label="Replaces in_charge with out_charge in all precursors" help=""> |
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236 <expand macro="list_string_san" name="replace_pc_charge"/> |
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237 </param> |
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238 <section name="blackorwhitelist" title="Black or white listing of of MS2 spectra by spectral similarity" help="" expanded="false"> |
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239 <param name="file" argument="-spectra:blackorwhitelist:file" type="data" format="mzml" optional="true" label="Input file containing MS2 spectra that should be retained or removed from the mzML file" help="Matching tolerances are taken from 'spectra:blackorwhitelist:similarity_threshold|rt|mz' options.. select mzml data sets(s)"/> |
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240 <param name="similarity_threshold" argument="-spectra:blackorwhitelist:similarity_threshold" type="float" min="-1.0" max="1.0" value="-1.0" label="Similarity threshold when matching MS2 spectra" help="(-1 = disabled)"/> |
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241 <param name="rt" argument="-spectra:blackorwhitelist:rt" type="float" value="0.01" label="Retention tolerance [s] when matching precursor positions" help="(-1 = disabled)"/> |
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242 <param name="mz" argument="-spectra:blackorwhitelist:mz" type="float" value="0.01" label="m/z tolerance [Th] when matching precursor positions" help="(-1 = disabled)"/> |
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243 <param name="use_ppm_tolerance" argument="-spectra:blackorwhitelist:use_ppm_tolerance" type="text" value="false" label="If ppm tolerance should be used" help="Otherwise Da are used"> |
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244 <expand macro="list_string_san" name="use_ppm_tolerance"/> |
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245 </param> |
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246 <param name="blacklist" argument="-spectra:blackorwhitelist:blacklist" type="boolean" truevalue="true" falsevalue="false" checked="true" label="True: remove matched MS2" help="False: retain matched MS2 spectra. Other levels are kept"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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247 </section> |
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248 </section> |
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249 <section name="feature" title="Feature data options" help="" expanded="false"> |
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250 <param name="q" argument="-feature:q" type="text" value=":" label="Overall quality range to extract [0:1]" help=""> |
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251 <expand macro="list_string_san" name="q"/> |
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252 </param> |
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253 </section> |
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254 <section name="consensus" title="Consensus feature data options" help="" expanded="false"> |
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255 <param name="map" argument="-consensus:map" type="text" optional="true" value="" label="Non-empty list of maps to be extracted from a consensus (indices are 0-based)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
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256 <expand macro="list_integer_valsan" name="map"/> |
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257 </param> |
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258 <param name="map_and" argument="-consensus:map_and" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" help=""/> |
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259 <section name="blackorwhitelist" title="Black or white listing of of MS2 spectra by consensus features" help="" expanded="false"> |
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260 <param name="blacklist" argument="-consensus:blackorwhitelist:blacklist" type="boolean" truevalue="true" falsevalue="false" checked="true" label="True: remove matched MS2" help="False: retain matched MS2 spectra. Other levels are kept"/> |
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261 <param name="file" argument="-consensus:blackorwhitelist:file" type="data" format="consensusxml" optional="true" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file" help="Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.. If consensus:blackorwhitelist:maps is specified, only these will be used.. select consensusxml data sets(s)"/> |
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262 <param name="maps" argument="-consensus:blackorwhitelist:maps" type="text" optional="true" value="" label="Maps used for black/white list filtering" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
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263 <expand macro="list_integer_valsan" name="maps"/> |
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264 </param> |
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265 <param name="rt" argument="-consensus:blackorwhitelist:rt" type="float" min="0.0" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help=""/> |
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266 <param name="mz" argument="-consensus:blackorwhitelist:mz" type="float" min="0.0" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help=""/> |
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267 <param name="use_ppm_tolerance" argument="-consensus:blackorwhitelist:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If ppm tolerance should be used" help="Otherwise Da are used"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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268 </section> |
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269 </section> |
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270 <section name="f_and_c" title="Feature & Consensus data options" help="" expanded="false"> |
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271 <param name="charge" argument="-f_and_c:charge" type="text" value=":" label="Charge range to extract" help=""> |
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272 <expand macro="list_string_san" name="charge"/> |
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273 </param> |
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274 <param name="size" argument="-f_and_c:size" type="text" value=":" label="Size range to extract" help=""> |
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275 <expand macro="list_string_san" name="size"/> |
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276 </param> |
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277 <param name="remove_meta" argument="-f_and_c:remove_meta" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. <name> 'lt|eq|gt' <value>; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
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278 <expand macro="list_string_val" name="remove_meta"/> |
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279 <expand macro="list_string_san" name="remove_meta"/> |
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280 </param> |
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281 <param name="remove_hull" argument="-f_and_c:remove_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove hull from features" help=""/> |
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282 </section> |
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283 <section name="id" title="ID options" help="The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist" expanded="false"> |
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284 <param name="remove_clashes" argument="-id:remove_clashes" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features with id clashes (different sequences mapped to one feature)" help=""/> |
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285 <param name="keep_best_score_id" argument="-id:keep_best_score_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="in case of multiple peptide identifications, keep only the id with best score" help=""/> |
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286 <param name="sequences_whitelist" argument="-id:sequences_whitelist" type="text" optional="true" value="" label="Keep only features containing whitelisted substrings" help="e.g. features containing LYSNLVER or the modification (Oxidation). To control comparison method used for whitelisting, see 'id:sequence_comparison_method' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
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287 <expand macro="list_string_val" name="sequences_whitelist"/> |
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288 <expand macro="list_string_san" name="sequences_whitelist"/> |
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289 </param> |
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290 <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" type="select" label="Comparison method used to determine if a feature is whitelisted" help=""> |
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291 <option value="substring" selected="true">substring</option> |
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292 <option value="exact">exact</option> |
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293 <expand macro="list_string_san" name="sequence_comparison_method"/> |
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294 </param> |
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295 <param name="accessions_whitelist" argument="-id:accessions_whitelist" type="text" optional="true" value="" label="keep only features with white listed accessions" help="e.g. sp|P02662|CASA1_BOVIN (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
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296 <expand macro="list_string_val" name="accessions_whitelist"/> |
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297 <expand macro="list_string_san" name="accessions_whitelist"/> |
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298 </param> |
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299 <param name="remove_annotated_features" argument="-id:remove_annotated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features with annotations" help=""/> |
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300 <param name="remove_unannotated_features" argument="-id:remove_unannotated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features without annotations" help=""/> |
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301 <param name="remove_unassigned_ids" argument="-id:remove_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassigned peptide identifications" help=""/> |
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302 <param name="blacklist" argument="-id:blacklist" type="data" format="idxml" optional="true" label="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file" help="Matching tolerances are taken from 'id:rt' and 'id:mz' options.. This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches select idxml data sets(s)"/> |
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303 <param name="rt" argument="-id:rt" type="float" min="0.0" value="0.1" label="Retention tolerance [s] for precursor to id position" help=""/> |
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304 <param name="mz" argument="-id:mz" type="float" min="0.0" value="0.001" label="m/z tolerance [Th] for precursor to id position" help=""/> |
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305 <param name="blacklist_imperfect" argument="-id:blacklist_imperfect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow for mismatching precursor positions (see 'id:blacklist')" help=""/> |
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306 </section> |
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307 <section name="algorithm" title="S/N algorithm section" help="" expanded="false"> |
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308 <section name="SignalToNoise" title="" help="" expanded="false"> |
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309 <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> |
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310 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/> |
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311 <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/> |
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312 <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help=""/> |
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313 <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/> |
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314 <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/> |
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315 <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/> |
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316 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/> |
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317 <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/> |
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318 </section> |
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319 </section> |
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320 <expand macro="adv_opts_macro"> |
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321 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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322 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
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323 <expand macro="list_string_san" name="test"/> |
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324 </param> |
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325 </expand> |
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326 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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327 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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328 </param> |
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329 </inputs> |
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330 <outputs> |
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331 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"> |
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332 <change_format> |
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333 <when input="out_type" value="featureXML" format="featurexml"/> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
334 <when input="out_type" value="mzML" format="mzml"/> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
335 </change_format> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
336 </data> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
337 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
338 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
|
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
339 </data> |
|
0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
340 </outputs> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
changeset
|
341 <tests> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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changeset
|
342 <!-- TOPP_FileFilter_1 --> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
343 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
344 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
345 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
346 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
347 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
348 <param name="in" value="FileFilter_1_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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changeset
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349 <output name="out" value="FileFilter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
350 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
351 <param name="rt" value=":30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
352 <param name="mz" value=":1000"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
353 <param name="int" value=":20000"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
354 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
355 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
356 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
357 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
358 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
359 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
360 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
361 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
362 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
363 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
364 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
365 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
366 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
367 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
368 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
369 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
370 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
371 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
372 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
373 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
374 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
375 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
376 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
377 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
378 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
379 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
380 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
381 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
382 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
383 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
384 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
385 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
386 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
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changeset
|
387 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
388 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
389 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
390 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
391 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
392 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
393 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
394 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
395 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
396 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
397 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
398 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
399 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
400 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
401 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
402 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
403 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
404 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
405 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
406 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
407 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
408 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
409 <param name="keep_best_score_id" value="false"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
410 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
411 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
412 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
413 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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414 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
415 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
416 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
417 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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418 <section name="algorithm"> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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419 <section name="SignalToNoise"> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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420 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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421 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
422 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
423 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
424 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
425 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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426 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
427 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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428 <param name="write_log_messages" value="true"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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429 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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430 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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431 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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432 <output name="ctd_out" ftype="xml"> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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433 <assert_contents> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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434 <is_valid_xml/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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435 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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436 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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changeset
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437 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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438 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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439 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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440 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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441 <!-- TOPP_FileFilter_2 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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442 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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443 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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444 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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445 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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446 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
447 <param name="in" value="FileFilter_1_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
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448 <output name="out" value="FileFilter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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449 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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450 <param name="rt" value="30:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
451 <param name="mz" value="1000:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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452 <param name="int" value="100:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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453 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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454 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
455 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
456 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
457 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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458 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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459 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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460 <param name="remove_chromatograms" value="false"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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461 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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462 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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463 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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464 <param name="indexed_file" value="true"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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465 <param name="zlib_compression" value="false"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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466 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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467 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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468 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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469 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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470 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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471 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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472 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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473 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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474 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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475 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
476 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
477 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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478 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
479 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
480 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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481 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
482 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
483 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
484 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
485 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
486 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
487 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
488 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
489 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
490 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
491 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
492 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
493 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
494 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
495 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
496 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
497 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
498 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
499 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
500 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
501 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
502 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
503 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
changeset
|
504 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
505 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
506 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
507 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
508 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
509 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
510 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
511 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
512 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
513 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
514 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
515 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
516 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
517 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
518 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
519 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
520 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
521 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
522 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
523 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
524 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
525 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
526 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
527 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
528 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
529 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
530 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
531 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
532 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
533 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
534 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
535 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
changeset
|
536 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
changeset
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537 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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changeset
|
538 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
539 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
540 <!-- TOPP_FileFilter_3 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
541 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
542 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
543 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
544 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
545 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
546 <param name="in" value="FileFilter_1_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
547 <output name="out" value="FileFilter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
548 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
549 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
550 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
551 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
552 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
553 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
554 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
555 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
556 <param name="level" value="2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
557 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
558 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
559 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
560 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
561 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
562 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
563 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
564 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
565 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
566 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
567 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
568 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
569 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
570 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
571 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
572 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
573 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
574 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
575 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
576 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
577 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
578 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
579 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
580 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
581 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
582 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
583 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
584 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
585 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
586 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
587 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
588 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
589 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
590 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
591 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
592 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
593 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
594 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
595 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
596 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
597 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
598 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
599 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
600 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
601 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
602 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
603 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
604 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
605 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
606 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
607 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
608 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
609 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
610 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
611 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
612 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
613 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
614 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
615 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
616 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
617 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
618 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
619 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
620 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
621 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
622 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
623 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
624 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
625 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
626 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
627 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
628 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
629 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
630 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
631 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
632 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
633 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
634 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
635 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
changeset
|
636 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
637 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
638 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
639 <!-- TOPP_FileFilter_4 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
640 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
641 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
642 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
643 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
644 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
645 <param name="in" value="FileFilter_4_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
changeset
|
646 <output name="out" value="FileFilter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
647 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
648 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
649 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
650 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
651 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
652 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
653 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
654 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
655 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
656 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
657 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
658 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
659 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
660 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
661 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
662 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
663 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
664 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
665 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
666 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
667 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
668 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
669 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
670 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
671 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
672 <param name="remove_zoom" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
673 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
674 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
675 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
676 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
677 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
678 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
679 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
680 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
681 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
682 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
683 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
684 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
685 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
686 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
687 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
688 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
689 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
690 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
691 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
692 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
693 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
694 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
695 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
696 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
697 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
698 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
699 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
700 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
701 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
702 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
703 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
704 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
705 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
706 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
707 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
708 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
709 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
710 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
711 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
712 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
713 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
714 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
715 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
716 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
717 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
718 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
719 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
720 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
721 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
722 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
723 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
724 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
725 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
726 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
727 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
728 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
729 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
730 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
731 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
732 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
733 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
734 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
735 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
736 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
737 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
738 <!-- TOPP_FileFilter_5 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
739 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
740 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
741 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
742 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
743 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
744 <param name="in" value="FileFilter_5_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
745 <output name="out" value="FileFilter_5_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
746 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
747 <param name="rt" value=":1000"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
748 <param name="mz" value=":480"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
749 <param name="int" value=":79000"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
750 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
751 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
752 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
753 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
754 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
755 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
756 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
757 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
758 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
759 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
760 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
761 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
762 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
763 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
764 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
765 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
766 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
767 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
768 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
769 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
770 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
771 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
772 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
773 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
774 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
775 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
776 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
777 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
778 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
779 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
780 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
781 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
782 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
783 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
784 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
785 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
786 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
787 <param name="q" value=":0.6"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
788 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
789 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
790 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
791 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
792 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
793 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
794 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
795 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
796 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
797 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
798 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
799 <param name="charge" value=":3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
800 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
801 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
802 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
803 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
804 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
805 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
806 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
807 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
808 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
809 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
810 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
811 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
812 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
813 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
814 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
815 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
816 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
817 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
818 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
819 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
820 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
821 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
822 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
823 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
824 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
825 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
826 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
827 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
828 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
829 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
830 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
831 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
832 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
833 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
834 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
835 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
836 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
837 <!-- TOPP_FileFilter_6 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
838 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
839 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
840 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
841 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
842 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
843 <param name="in" value="FileFilter_5_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
844 <output name="out" value="FileFilter_6_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
845 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
846 <param name="rt" value="1000:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
847 <param name="mz" value="440:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
848 <param name="int" value="70000:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
849 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
850 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
851 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
852 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
853 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
854 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
855 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
856 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
857 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
858 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
859 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
860 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
861 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
862 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
863 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
864 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
865 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
866 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
867 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
868 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
869 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
870 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
871 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
872 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
873 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
874 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
875 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
876 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
877 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
878 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
879 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
880 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
881 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
882 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
883 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
884 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
885 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
886 <param name="q" value="0.51:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
887 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
888 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
889 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
890 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
891 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
892 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
893 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
894 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
895 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
896 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
897 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
898 <param name="charge" value="3:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
899 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
900 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
901 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
902 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
903 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
904 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
905 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
906 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
907 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
908 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
909 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
910 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
911 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
912 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
913 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
914 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
915 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
916 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
917 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
918 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
919 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
920 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
921 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
922 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
923 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
924 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
925 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
926 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
927 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
928 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
929 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
930 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
931 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
932 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
933 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
934 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
935 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
936 <!-- TOPP_FileFilter_7 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
937 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
938 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
939 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
940 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
941 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
942 <param name="in" value="FileFilter_7_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
943 <output name="out" value="FileFilter_7_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
944 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
945 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
946 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
947 <param name="int" value="7000:"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
948 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
949 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
950 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
951 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
952 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
953 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
954 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
955 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
956 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
957 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
958 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
959 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
960 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
961 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
962 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
963 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
964 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
965 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
966 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
967 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
968 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
969 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
970 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
971 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
972 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
973 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
974 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
975 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
976 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
977 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
978 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
979 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
980 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
981 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
982 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
983 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
984 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
985 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
986 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
987 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
988 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
989 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
990 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
991 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
992 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
993 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
994 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
995 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
996 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
997 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
998 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
999 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1000 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1001 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1002 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1003 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1004 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1005 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1006 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1007 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1008 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1009 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1010 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1011 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1012 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1013 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1014 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1015 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1016 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1017 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1018 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1019 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1020 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1021 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1022 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1023 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1024 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1025 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1026 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1027 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1028 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1029 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1030 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1031 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1032 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1033 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1034 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1035 <!-- TOPP_FileFilter_8 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1036 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1037 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1038 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1039 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1040 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1041 <param name="in" value="FileFilter_8_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1042 <output name="out" value="FileFilter_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1043 <param name="out_type" value="consensusXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1044 <param name="rt" value="600:1400"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1045 <param name="mz" value="700:2300"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1046 <param name="int" value="1100:6000"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1047 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1048 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1049 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1050 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1051 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1052 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1053 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1054 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1055 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1056 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1057 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1058 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1059 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1060 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1061 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1062 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1063 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1064 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1065 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1066 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1067 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1068 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1069 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1070 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1071 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1072 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1073 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1074 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1075 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1076 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1077 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1078 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1079 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1080 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1081 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1082 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1083 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1084 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1085 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1086 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1087 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1088 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1089 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1090 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1091 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1092 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1093 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1094 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1095 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1096 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1097 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1098 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1099 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1100 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1101 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1102 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1103 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1104 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1105 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1106 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1107 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1108 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1109 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1110 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1111 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1112 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1113 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1114 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1115 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1116 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1117 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1118 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1119 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1120 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1121 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1122 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1123 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1124 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1125 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1126 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1127 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1128 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1129 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1130 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1131 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1132 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1133 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1134 <!-- TOPP_FileFilter_9 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1135 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1136 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1137 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1138 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1139 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1140 <param name="in" value="FileFilter_9_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1141 <output name="out" value="FileFilter_9_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1142 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1143 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1144 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1145 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1146 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1147 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1148 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1149 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1150 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1151 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1152 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1153 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1154 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1155 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1156 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1157 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1158 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1159 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1160 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1161 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1162 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1163 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1164 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1165 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1166 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1167 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1168 <param name="remove_mode" value="SelectedIonMonitoring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1169 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1170 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1171 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1172 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1173 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1174 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1175 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1176 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1177 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1178 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1179 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1180 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1181 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1182 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1183 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1184 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1185 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1186 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1187 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1188 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1189 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1190 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1191 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1192 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1193 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1194 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1195 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1196 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1197 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1198 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1199 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1200 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1201 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1202 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1203 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1204 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1205 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1206 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1207 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1208 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1209 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1210 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1211 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1212 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1213 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1214 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1215 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1216 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1217 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1218 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1219 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1220 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1221 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1222 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1223 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1224 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1225 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1226 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1227 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1228 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1229 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1230 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1231 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1232 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1233 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1234 <!-- TOPP_FileFilter_10 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1235 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1236 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1237 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1238 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1239 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1240 <param name="in" value="FileFilter_10_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1241 <output name="out" value="FileFilter_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1242 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1243 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1244 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1245 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1246 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1247 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1248 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1249 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1250 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1251 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1252 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1253 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1254 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1255 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1256 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1257 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1258 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1259 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1260 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1261 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1262 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1263 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1264 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1265 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1266 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1267 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1268 <param name="remove_activation" value="Collision-induced dissociation"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1269 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1270 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1271 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1272 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1273 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1274 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1275 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1276 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1277 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1278 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1279 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1280 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1281 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1282 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1283 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1284 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1285 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1286 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1287 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1288 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1289 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1290 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1291 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1292 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1293 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1294 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1295 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1296 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1297 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1298 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1299 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1300 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1301 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1302 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1303 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1304 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1305 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1306 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1307 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1308 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1309 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1310 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1311 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1312 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1313 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1314 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1315 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1316 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1317 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1318 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1319 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1320 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1321 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1322 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1323 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1324 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1325 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1326 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1327 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1328 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1329 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1330 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1331 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1332 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1333 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1334 <!-- TOPP_FileFilter_11 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1335 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1336 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1337 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1338 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1339 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1340 <param name="in" value="FileFilter_11_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1341 <output name="out" value="FileFilter_11_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1342 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1343 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1344 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1345 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1346 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1347 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1348 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1349 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1350 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1351 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1352 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1353 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1354 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1355 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1356 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1357 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1358 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1359 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1360 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1361 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1362 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1363 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1364 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1365 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1366 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1367 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1368 <param name="remove_activation" value="Plasma desorption"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1369 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1370 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1371 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1372 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1373 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1374 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1375 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1376 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1377 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1378 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1379 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1380 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1381 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1382 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1383 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1384 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1385 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1386 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1387 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1388 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1389 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1390 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1391 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1392 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1393 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1394 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1395 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1396 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1397 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1398 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1399 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1400 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1401 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1402 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1403 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1404 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1405 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1406 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1407 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1408 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1409 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1410 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1411 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1412 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1413 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1414 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1415 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1416 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1417 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1418 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1419 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1420 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1421 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1422 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1423 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1424 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1425 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1426 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1427 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1428 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1429 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1430 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1431 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1432 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1433 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1434 <!-- TOPP_FileFilter_12 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1435 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1436 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1437 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1438 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1439 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1440 <param name="in" value="FileFilter_12_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1441 <output name="out" value="FileFilter_12_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1442 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1443 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1444 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1445 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1446 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1447 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1448 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1449 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1450 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1451 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1452 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1453 <param name="remove_chromatograms" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1454 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1455 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1456 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1457 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1458 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1459 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1460 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1461 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1462 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1463 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1464 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1465 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1466 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1467 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1468 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1469 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1470 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1471 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1472 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1473 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1474 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1475 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1476 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1477 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1478 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1479 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1480 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1481 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1482 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1483 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1484 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1485 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1486 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1487 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1488 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1489 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1490 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1491 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1492 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1493 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1494 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1495 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1496 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1497 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1498 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1499 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1500 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1501 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1502 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1503 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1504 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1505 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1506 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1507 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1508 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1509 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1510 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1511 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1512 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1513 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1514 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1515 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1516 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1517 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1518 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1519 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1520 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1521 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1522 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1523 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1524 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1525 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1526 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1527 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1528 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1529 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1530 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1531 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1532 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1533 <!-- TOPP_FileFilter_13 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1534 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1535 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1536 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1537 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1538 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1539 <param name="in" value="FileFilter_13_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1540 <output name="out" value="FileFilter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1541 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1542 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1543 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1544 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1545 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1546 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1547 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1548 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1549 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1550 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1551 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1552 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1553 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1554 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1555 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1556 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1557 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1558 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1559 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1560 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1561 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1562 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1563 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1564 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1565 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1566 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1567 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1568 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1569 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1570 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1571 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1572 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1573 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1574 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1575 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1576 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1577 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1578 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1579 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1580 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1581 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1582 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1583 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1584 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1585 <param name="map" value="2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1586 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1587 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1588 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1589 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1590 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1591 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1592 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1593 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1594 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1595 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1596 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1597 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1598 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1599 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1600 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1601 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1602 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1603 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1604 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1605 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1606 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1607 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1608 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1609 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1610 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1611 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1612 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1613 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1614 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1615 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1616 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1617 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1618 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1619 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1620 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1621 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1622 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1623 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1624 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1625 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1626 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1627 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1628 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1629 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1630 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1631 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1632 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1633 <!-- TOPP_FileFilter_14 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1634 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1635 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1636 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1637 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1638 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1639 <param name="in" value="FileFilter_14_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1640 <output name="out" value="FileFilter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1641 <param name="out_type" value="consensusXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1642 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1643 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1644 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1645 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1646 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1647 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1648 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1649 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1650 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1651 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1652 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1653 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1654 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1655 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1656 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1657 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1658 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1659 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1660 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1661 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1662 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1663 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1664 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1665 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1666 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1667 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1668 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1669 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1670 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1671 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1672 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1673 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1674 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1675 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1676 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1677 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1678 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1679 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1680 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1681 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1682 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1683 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1684 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1685 <param name="map" value="0 2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1686 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1687 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1688 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1689 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1690 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1691 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1692 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1693 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1694 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1695 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1696 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1697 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1698 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1699 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1700 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1701 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1702 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1703 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1704 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1705 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1706 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1707 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1708 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1709 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1710 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1711 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1712 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1713 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1714 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1715 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1716 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1717 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1718 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1719 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1720 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1721 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1722 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1723 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1724 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1725 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1726 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1727 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1728 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1729 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1730 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1731 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1732 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1733 <!-- TOPP_FileFilter_15 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1734 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1735 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1736 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1737 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1738 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1739 <param name="in" value="FileFilter_15_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1740 <output name="out" value="FileFilter_15_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1741 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1742 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1743 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1744 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1745 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1746 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1747 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1748 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1749 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1750 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1751 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1752 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1753 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1754 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1755 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1756 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1757 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1758 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1759 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1760 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1761 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1762 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1763 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1764 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1765 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1766 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1767 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1768 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1769 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1770 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1771 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1772 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1773 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1774 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1775 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1776 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1777 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1778 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1779 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1780 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1781 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1782 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1783 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1784 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1785 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1786 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1787 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1788 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1789 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1790 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1791 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1792 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1793 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1794 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1795 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1796 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1797 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1798 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1799 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1800 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1801 <param name="sequences_whitelist" value=""Oxidation""/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1802 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1803 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1804 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1805 <param name="remove_unassigned_ids" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1806 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1807 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1808 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1809 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1810 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1811 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1812 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1813 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1814 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1815 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1816 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1817 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1818 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1819 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1820 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1821 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1822 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1823 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1824 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1825 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1826 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1827 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1828 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1829 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1830 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1831 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1832 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1833 <!-- TOPP_FileFilter_16 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1834 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1835 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1836 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1837 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1838 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1839 <param name="in" value="FileFilter_15_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1840 <output name="out" value="FileFilter_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1841 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1842 <param name="rt" value="3000:4000"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1843 <param name="mz" value="400:600"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1844 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1845 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1846 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1847 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1848 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1849 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1850 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1851 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1852 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1853 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1854 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1855 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1856 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1857 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1858 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1859 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1860 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1861 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1862 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1863 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1864 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1865 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1866 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1867 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1868 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1869 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1870 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1871 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1872 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1873 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1874 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1875 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1876 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1877 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1878 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1879 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1880 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1881 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1882 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1883 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1884 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1885 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1886 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1887 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1888 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1889 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1890 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1891 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1892 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1893 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1894 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1895 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
1896 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1897 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1898 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1899 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1900 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1901 <param name="sequences_whitelist" value=""Oxidation""/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1902 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1903 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1904 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1905 <param name="remove_unassigned_ids" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1906 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1907 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1908 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1909 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1910 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1911 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1912 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1913 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1914 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1915 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1916 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1917 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
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|
1918 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1919 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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|
1920 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
1921 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1922 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
1923 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1924 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
|
1925 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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1926 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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|
1927 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents:
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1928 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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1929 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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1930 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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1931 </assert_stdout> |
|
15
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1932 </test> |
|
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1933 <!-- TOPP_FileFilter_17 --> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
|
1934 <test expect_num_outputs="2"> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents:
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diff
changeset
|
1935 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
|
1936 <param name="force" value="false"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
|
1937 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff
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1938 </section> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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|
1939 <param name="in" value="FileFilter_15_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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|
1940 <output name="out" value="FileFilter_17_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff
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|
1941 <param name="out_type" value="featureXML"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
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1942 <param name="rt" value="3000:4000"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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1943 <param name="mz" value="400:600"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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1944 <param name="int" value=":"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1945 <param name="sort" value="false"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1946 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1947 <param name="sn" value="0.0"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1948 <param name="pc_mz_range" value=":"/> |
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1949 <param name="level" value="1 2 3"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1950 <param name="sort_peaks" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1951 <param name="no_chromatograms" value="false"/> |
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1952 <param name="remove_chromatograms" value="false"/> |
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1953 <param name="remove_empty" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1954 <param name="mz_precision" value="64"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1955 <param name="int_precision" value="32"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1956 <param name="indexed_file" value="true"/> |
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1957 <param name="zlib_compression" value="false"/> |
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1958 <section name="numpress"> |
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1959 <param name="masstime" value="none"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1960 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
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1961 <param name="intensity" value="none"/> |
|
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1962 <param name="float_da" value="none"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1963 </section> |
|
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1964 </section> |
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1965 <section name="spectra"> |
|
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1966 <param name="remove_zoom" value="false"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1967 <param name="remove_collision_energy" value=":"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1968 <param name="remove_isolation_window_width" value=":"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1969 <param name="select_zoom" value="false"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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1970 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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1971 <param name="select_isolation_window_width" value=":"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1972 <param name="replace_pc_charge" value=":"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1973 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1974 <param name="similarity_threshold" value="-1.0"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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1975 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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1976 <param name="mz" value="0.01"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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1977 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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1978 <param name="blacklist" value="true"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1979 </section> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1980 </section> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1981 <section name="feature"> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1982 <param name="q" value=":"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1983 </section> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1984 <section name="consensus"> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1985 <param name="map_and" value="false"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1986 <section name="blackorwhitelist"> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1987 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
1988 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
1989 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
1990 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1991 </section> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1992 </section> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1993 <section name="f_and_c"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1994 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1995 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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changeset
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1996 <param name="remove_hull" value="false"/> |
|
15
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
1997 </section> |
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fe4e4587d265
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galaxyp
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changeset
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1998 <section name="id"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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1999 <param name="remove_clashes" value="false"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
|
2000 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2001 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2002 <param name="remove_annotated_features" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2003 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2004 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2005 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2006 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2007 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2008 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2009 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2010 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2011 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2012 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2013 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2014 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2015 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
2016 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2017 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2018 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2019 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2020 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2021 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2022 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2023 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2024 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2025 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2026 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2027 </output> |
|
16
86a9dd43dd09
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galaxyp
parents:
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diff
changeset
|
2028 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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|
2029 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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|
2030 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2031 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2032 <!-- TOPP_FileFilter_18 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2033 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
2034 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
2035 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2036 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2037 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2038 <param name="in" value="FileFilter_18_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
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diff
changeset
|
2039 <output name="out" value="FileFilter_18_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
2040 <param name="out_type" value="consensusXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2041 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2042 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2043 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
2044 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2045 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2046 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2047 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
2048 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2049 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2050 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2051 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2052 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2053 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2054 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2055 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2056 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2057 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2058 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2059 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2060 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2061 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2062 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2063 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2064 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2065 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2066 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2067 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2068 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2069 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2070 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2071 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2072 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2073 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2074 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2075 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2076 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2077 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2078 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2079 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2080 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2081 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2082 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2083 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2084 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2085 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2086 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2087 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2088 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2089 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2090 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2091 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2092 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2093 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2094 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2095 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2096 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2097 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2098 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2099 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2100 <param name="sequences_whitelist" value=""Oxidation""/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2101 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2102 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2103 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2104 <param name="remove_unassigned_ids" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2105 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2106 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2107 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2108 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2109 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2110 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2111 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2112 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2113 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2114 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2115 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2116 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2117 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2118 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2119 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2120 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2121 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2122 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2123 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2124 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2125 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2126 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2127 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2128 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2129 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2130 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2131 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2132 <!-- TOPP_FileFilter_19 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2133 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2134 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2135 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2136 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2137 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2138 <param name="in" value="FileFilter_18_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2139 <output name="out" value="FileFilter_19_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2140 <param name="out_type" value="consensusXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2141 <param name="rt" value="3000:4000"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2142 <param name="mz" value="400:600"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2143 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2144 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2145 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2146 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2147 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2148 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2149 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2150 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2151 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2152 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2153 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2154 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2155 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2156 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2157 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2158 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2159 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2160 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2161 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2162 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2163 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2164 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2165 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2166 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2167 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2168 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2169 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2170 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2171 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2172 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2173 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2174 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2175 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2176 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2177 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2178 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2179 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2180 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2181 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2182 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2183 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2184 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2185 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2186 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2187 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2188 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2189 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2190 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2191 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2192 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2193 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2194 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2195 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2196 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2197 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2198 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2199 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2200 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2201 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2202 <param name="remove_unannotated_features" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2203 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2204 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2205 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2206 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2207 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2208 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2209 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2210 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2211 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2212 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2213 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2214 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2215 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2216 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2217 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2218 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2219 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2220 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2221 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2222 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2223 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2224 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2225 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2226 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2227 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2228 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2229 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2230 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2231 <!-- TOPP_FileFilter_20 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2232 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2233 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2234 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2235 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2236 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2237 <param name="in" value="FileFilter_15_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2238 <output name="out" value="FileFilter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2239 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2240 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2241 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2242 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2243 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2244 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2245 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2246 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2247 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2248 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2249 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2250 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2251 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2252 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2253 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2254 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2255 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2256 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2257 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2258 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2259 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2260 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2261 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2262 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2263 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2264 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2265 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2266 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2267 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2268 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2269 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2270 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2271 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2272 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2273 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2274 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2275 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2276 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2277 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2278 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2279 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2280 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2281 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2282 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2283 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2284 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2285 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2286 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2287 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2288 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2289 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2290 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2291 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2292 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2293 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2294 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2295 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2296 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2297 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2298 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2299 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2300 <param name="accessions_whitelist" value=""YDL217C""/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2301 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2302 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2303 <param name="remove_unassigned_ids" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2304 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2305 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2306 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2307 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2308 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2309 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2310 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2311 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2312 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2313 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2314 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2315 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2316 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2317 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2318 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2319 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2320 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2321 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2322 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2323 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2324 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2325 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2326 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2327 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2328 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2329 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2330 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2331 <!-- TOPP_FileFilter_21 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2332 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2333 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2334 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2335 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2336 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2337 <param name="in" value="FileFilter_15_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2338 <output name="out" value="FileFilter_21_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2339 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2340 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2341 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2342 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2343 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2344 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2345 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2346 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2347 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2348 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2349 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2350 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2351 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2352 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2353 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2354 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2355 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2356 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2357 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2358 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2359 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2360 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2361 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2362 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2363 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2364 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2365 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2366 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2367 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2368 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2369 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2370 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2371 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2372 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2373 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2374 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2375 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2376 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2377 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2378 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2379 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2380 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2381 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2382 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2383 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2384 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2385 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2386 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2387 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2388 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2389 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2390 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2391 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2392 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2393 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2394 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2395 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2396 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2397 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2398 <param name="keep_best_score_id" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2399 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2400 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2401 <param name="remove_unannotated_features" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2402 <param name="remove_unassigned_ids" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2403 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2404 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2405 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2406 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2407 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2408 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2409 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2410 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2411 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2412 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2413 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2414 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2415 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2416 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2417 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2418 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2419 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2420 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2421 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2422 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2423 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2424 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2425 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2426 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2427 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2428 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2429 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2430 <!-- TOPP_FileFilter_22 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2431 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2432 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2433 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2434 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2435 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2436 <param name="in" value="FileFilter_22_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2437 <output name="out" value="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2438 <param name="out_type" value="consensusXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2439 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2440 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2441 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2442 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2443 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2444 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2445 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2446 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2447 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2448 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2449 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2450 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2451 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2452 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2453 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2454 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2455 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2456 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2457 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2458 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2459 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2460 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2461 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2462 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2463 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2464 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2465 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2466 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2467 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2468 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2469 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2470 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2471 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2472 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2473 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2474 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2475 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2476 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2477 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2478 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2479 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2480 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2481 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2482 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2483 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2484 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2485 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2486 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2487 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2488 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2489 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2490 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2491 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2492 <param name="size" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2493 <param name="remove_meta" value=""distinct_charges" "gt" "1,2""/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2494 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2495 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2496 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2497 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2498 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2499 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2500 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2501 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2502 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2503 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2504 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2505 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2506 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2507 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2508 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2509 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2510 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2511 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2512 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2513 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2514 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2515 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2516 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2517 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2518 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2519 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2520 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2521 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2522 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2523 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2524 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2525 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2526 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2527 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2528 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2529 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2530 <!-- TOPP_FileFilter_23 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2531 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2532 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2533 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2534 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2535 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2536 <param name="in" value="FileFilter_22_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2537 <output name="out" value="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2538 <param name="out_type" value="consensusXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2539 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2540 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2541 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2542 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2543 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2544 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2545 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2546 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2547 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2548 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2549 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2550 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2551 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2552 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2553 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2554 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2555 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2556 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2557 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2558 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2559 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2560 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2561 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2562 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2563 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2564 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2565 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2566 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2567 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2568 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2569 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2570 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2571 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2572 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2573 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2574 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2575 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2576 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2577 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2578 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2579 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2580 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2581 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2582 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2583 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2584 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2585 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2586 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2587 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2588 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2589 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2590 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2591 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2592 <param name="size" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2593 <param name="remove_meta" value=""distinct_charges_size" "gt" "2""/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2594 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2595 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2596 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2597 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2598 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2599 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2600 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2601 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2602 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2603 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2604 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2605 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2606 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2607 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2608 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2609 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2610 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2611 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2612 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2613 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2614 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2615 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2616 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2617 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2618 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2619 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2620 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2621 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2622 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2623 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2624 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2625 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2626 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2627 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2628 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2629 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2630 <!-- TOPP_FileFilter_24 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2631 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2632 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2633 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2634 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2635 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2636 <param name="in" value="FileFilter_22_input.consensusXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2637 <output name="out" value="FileFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2638 <param name="out_type" value="consensusXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2639 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2640 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2641 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2642 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2643 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2644 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2645 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2646 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2647 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2648 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2649 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2650 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2651 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2652 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2653 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2654 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2655 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2656 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2657 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2658 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2659 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2660 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2661 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2662 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2663 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2664 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2665 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2666 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2667 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2668 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2669 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2670 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2671 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2672 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2673 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2674 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2675 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2676 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2677 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2678 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2679 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2680 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2681 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2682 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2683 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2684 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2685 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2686 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2687 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2688 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2689 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2690 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2691 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2692 <param name="size" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2693 <param name="remove_meta" value=""DOESNOTEXIST" "lt" "whatever""/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2694 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2695 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2696 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2697 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2698 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2699 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2700 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2701 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2702 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2703 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2704 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2705 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2706 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2707 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2708 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2709 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2710 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2711 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2712 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2713 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2714 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2715 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2716 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2717 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2718 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2719 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2720 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2721 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2722 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2723 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2724 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2725 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2726 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2727 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2728 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2729 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2730 <!-- TOPP_FileFilter_25 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2731 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2732 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2733 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2734 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2735 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2736 <param name="in" value="FileFilter_25_input.mzML.gz"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2737 <output name="out" value="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2738 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2739 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2740 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2741 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2742 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2743 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2744 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2745 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2746 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2747 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2748 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2749 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2750 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2751 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2752 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2753 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2754 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2755 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2756 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2757 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2758 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2759 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2760 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2761 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2762 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2763 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2764 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2765 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2766 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2767 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2768 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2769 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2770 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2771 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2772 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2773 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2774 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2775 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2776 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2777 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2778 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2779 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2780 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2781 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2782 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2783 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2784 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2785 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2786 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2787 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2788 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2789 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2790 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2791 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2792 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2793 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2794 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2795 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2796 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2797 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2798 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2799 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2800 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2801 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2802 <param name="blacklist" value="FileFilter_25_input.idXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2803 <param name="rt" value="1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2804 <param name="mz" value="0.05"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2805 <param name="blacklist_imperfect" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2806 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2807 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2808 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2809 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2810 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2811 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2812 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2813 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2814 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2815 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2816 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2817 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2818 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2819 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2820 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2821 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2822 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2823 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2824 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2825 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2826 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2827 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2828 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2829 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2830 <!-- TOPP_FileFilter_26 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2831 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2832 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2833 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2834 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2835 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2836 <param name="in" value="FileFilter_25_input.mzML.gz"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2837 <output name="out" value="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2838 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2839 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2840 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2841 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2842 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2843 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2844 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2845 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2846 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2847 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2848 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2849 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2850 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2851 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2852 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2853 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2854 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2855 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2856 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2857 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2858 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2859 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2860 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2861 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2862 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2863 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2864 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2865 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2866 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2867 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2868 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2869 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2870 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2871 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2872 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2873 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2874 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2875 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2876 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2877 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2878 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2879 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2880 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2881 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2882 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2883 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2884 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2885 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2886 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2887 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2888 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2889 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2890 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2891 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2892 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2893 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2894 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2895 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2896 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2897 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2898 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2899 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2900 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2901 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2902 <param name="blacklist" value="FileFilter_25_input.idXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2903 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2904 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2905 <param name="blacklist_imperfect" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2906 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2907 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2908 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2909 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2910 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2911 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2912 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2913 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2914 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2915 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2916 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2917 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2918 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2919 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2920 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2921 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2922 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2923 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2924 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2925 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2926 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2927 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2928 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2929 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2930 <!-- TOPP_FileFilter_28 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2931 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2932 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2933 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2934 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2935 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2936 <param name="in" value="FileFilter_28_input.mzML.gz"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2937 <output name="out" value="FileFilter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2938 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2939 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2940 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2941 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2942 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2943 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2944 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2945 <param name="pc_mz_range" value="832:836"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2946 <param name="level" value="2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2947 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2948 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2949 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2950 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2951 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2952 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2953 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2954 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2955 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2956 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2957 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2958 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2959 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2960 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2961 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2962 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2963 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2964 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2965 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2966 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2967 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2968 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2969 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2970 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2971 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2972 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2973 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2974 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2975 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2976 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2977 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2978 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2979 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2980 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2981 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2982 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2983 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2984 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2985 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2986 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2987 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2988 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2989 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2990 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2991 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2992 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2993 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2994 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2995 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2996 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2997 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2998 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2999 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3000 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3001 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3002 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3003 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3004 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3005 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3006 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3007 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3008 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3009 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3010 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3011 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3012 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3013 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3014 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3015 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3016 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3017 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3018 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3019 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3020 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3021 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3022 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3023 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3024 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3025 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3026 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3027 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3028 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3029 <!-- TOPP_FileFilter_29 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3030 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3031 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3032 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3033 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3034 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3035 <param name="in" value="FileFilter_28_input.mzML.gz"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3036 <output name="out" value="FileFilter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3037 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3038 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3039 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3040 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3041 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3042 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3043 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3044 <param name="pc_mz_range" value="832:836"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3045 <param name="level" value="1 2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3046 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3047 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3048 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3049 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3050 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3051 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3052 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3053 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3054 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3055 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3056 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3057 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3058 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3059 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3060 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3061 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3062 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3063 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3064 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3065 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3066 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3067 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3068 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3069 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3070 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3071 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3072 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3073 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3074 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3075 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3076 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3077 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3078 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3079 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3080 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3081 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3082 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3083 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3084 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3085 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3086 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3087 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3088 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3089 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3090 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3091 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3092 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3093 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3094 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3095 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3096 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3097 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3098 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3099 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3100 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3101 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3102 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3103 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3104 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3105 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3106 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3107 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3108 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3109 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3110 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3111 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3112 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3113 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3114 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3115 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3116 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3117 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3118 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3119 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3120 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3121 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3122 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3123 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3124 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3125 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3126 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3127 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3128 <!-- TOPP_FileFilter_30 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3129 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3130 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3131 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3132 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3133 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3134 <param name="in" value="FileFilter_28_input.mzML.gz"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3135 <output name="out" value="FileFilter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3136 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3137 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3138 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3139 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3140 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3141 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3142 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3143 <param name="pc_mz_range" value="832:836"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3144 <param name="level" value="1 2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3145 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3146 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3147 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3148 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3149 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3150 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3151 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3152 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3153 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3154 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3155 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3156 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3157 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3158 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3159 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3160 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3161 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3162 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3163 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3164 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3165 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3166 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3167 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3168 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3169 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3170 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3171 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3172 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3173 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3174 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3175 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3176 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3177 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3178 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3179 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3180 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3181 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3182 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3183 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3184 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3185 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3186 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3187 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3188 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3189 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3190 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3191 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3192 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3193 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3194 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3195 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3196 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3197 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3198 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3199 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3200 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3201 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3202 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3203 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3204 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3205 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3206 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3207 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3208 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3209 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3210 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3211 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3212 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3213 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3214 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3215 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3216 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3217 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3218 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3219 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3220 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3221 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3222 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3223 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3224 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3225 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3226 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3227 <!-- TOPP_FileFilter_31 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3228 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3229 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3230 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3231 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3232 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3233 <param name="in" value="FileFilter_31_34_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3234 <output name="out" value="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3235 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3236 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3237 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3238 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3239 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3240 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3241 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3242 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3243 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3244 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3245 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3246 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3247 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3248 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3249 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3250 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3251 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3252 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3253 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3254 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3255 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3256 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3257 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3258 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3259 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3260 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3261 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3262 <param name="remove_isolation_window_width" value=":2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3263 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3264 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3265 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3266 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3267 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3268 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3269 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3270 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3271 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3272 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3273 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3274 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3275 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3276 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3277 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3278 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3279 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3280 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3281 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3282 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3283 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3284 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3285 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3286 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3287 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3288 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3289 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3290 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3291 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3292 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3293 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3294 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3295 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3296 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3297 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3298 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3299 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3300 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3301 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3302 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3303 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3304 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3305 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3306 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3307 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3308 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3309 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3310 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3311 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3312 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3313 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3314 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3315 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3316 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3317 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3318 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3319 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3320 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3321 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3322 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3323 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3324 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3325 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3326 <!-- TOPP_FileFilter_32 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3327 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3328 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3329 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3330 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3331 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3332 <param name="in" value="FileFilter_31_34_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3333 <output name="out" value="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3334 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3335 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3336 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3337 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3338 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3339 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3340 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3341 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3342 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3343 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3344 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3345 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3346 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3347 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3348 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3349 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3350 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3351 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3352 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3353 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3354 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3355 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3356 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3357 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3358 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3359 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3360 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3361 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3362 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3363 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3364 <param name="select_isolation_window_width" value=":2"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3365 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3366 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3367 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3368 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3369 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3370 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3371 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3372 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3373 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3374 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3375 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3376 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3377 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3378 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3379 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3380 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3381 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3382 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3383 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3384 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3385 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3386 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3387 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3388 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3389 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3390 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3391 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3392 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3393 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3394 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3395 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3396 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3397 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3398 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3399 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3400 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3401 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3402 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3403 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3404 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3405 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3406 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3407 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3408 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3409 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3410 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3411 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3412 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3413 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3414 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3415 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3416 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3417 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3418 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3419 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3420 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3421 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3422 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3423 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3424 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3425 <!-- TOPP_FileFilter_33 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3426 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3427 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3428 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3429 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3430 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3431 <param name="in" value="FileFilter_31_34_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3432 <output name="out" value="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3433 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3434 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3435 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3436 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3437 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3438 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3439 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3440 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3441 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3442 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3443 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3444 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3445 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3446 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3447 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3448 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3449 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3450 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3451 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3452 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3453 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3454 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3455 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3456 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3457 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3458 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3459 <param name="remove_collision_energy" value=":35"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3460 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3461 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3462 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3463 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3464 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3465 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3466 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3467 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3468 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3469 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3470 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3471 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3472 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3473 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3474 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3475 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3476 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3477 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3478 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3479 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3480 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3481 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3482 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3483 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3484 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3485 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3486 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3487 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3488 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3489 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3490 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3491 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3492 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3493 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3494 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3495 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3496 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3497 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3498 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3499 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3500 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3501 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3502 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3503 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3504 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3505 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3506 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3507 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3508 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3509 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3510 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3511 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3512 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3513 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3514 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3515 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3516 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3517 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3518 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3519 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3520 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3521 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3522 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3523 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3524 <!-- TOPP_FileFilter_34 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3525 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3526 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3527 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3528 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3529 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3530 <param name="in" value="FileFilter_31_34_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3531 <output name="out" value="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3532 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3533 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3534 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3535 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3536 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3537 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3538 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3539 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3540 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3541 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3542 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3543 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3544 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3545 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3546 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3547 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3548 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3549 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3550 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3551 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3552 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3553 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3554 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3555 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3556 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3557 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3558 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3559 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3560 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3561 <param name="select_collision_energy" value=":35"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3562 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3563 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3564 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3565 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3566 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3567 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3568 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3569 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3570 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3571 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3572 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3573 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3574 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3575 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3576 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3577 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3578 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3579 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3580 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3581 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3582 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3583 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3584 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3585 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3586 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3587 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3588 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3589 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3590 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3591 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3592 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3593 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3594 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3595 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3596 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3597 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3598 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3599 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3600 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3601 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3602 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3603 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3604 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3605 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3606 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3607 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3608 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3609 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3610 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3611 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3612 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3613 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3614 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3615 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3616 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3617 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3618 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3619 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3620 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3621 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3622 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3623 <!-- TOPP_FileFilter_35 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3624 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3625 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3626 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3627 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3628 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3629 <param name="in" value="FileFilter_1_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3630 <output name="out" value="FileFilter_35_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3631 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3632 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3633 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3634 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3635 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3636 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3637 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3638 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3639 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3640 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3641 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3642 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3643 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3644 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3645 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3646 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3647 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3648 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3649 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3650 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3651 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3652 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3653 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3654 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3655 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3656 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3657 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3658 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3659 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3660 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3661 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3662 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3663 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3664 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3665 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3666 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3667 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3668 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3669 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3670 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3671 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3672 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3673 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3674 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3675 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3676 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3677 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3678 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3679 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3680 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3681 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3682 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3683 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3684 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3685 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3686 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3687 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3688 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3689 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3690 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3691 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3692 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3693 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3694 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3695 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3696 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3697 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3698 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3699 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3700 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3701 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3702 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3703 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3704 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3705 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3706 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3707 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3708 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3709 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3710 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3711 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3712 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3713 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3714 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3715 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3716 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3717 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3718 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3719 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3720 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3721 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3722 <!-- TOPP_FileFilter_36 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3723 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3724 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3725 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3726 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3727 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3728 <param name="in" value="FileFilter_1_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3729 <output name="out" value="FileFilter_36_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3730 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3731 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3732 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3733 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3734 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3735 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3736 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3737 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3738 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3739 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3740 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3741 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3742 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3743 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3744 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3745 <param name="indexed_file" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3746 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3747 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3748 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3749 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3750 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3751 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3752 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3753 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3754 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3755 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3756 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3757 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3758 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3759 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3760 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3761 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3762 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3763 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3764 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3765 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3766 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3767 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3768 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3769 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3770 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3771 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3772 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3773 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3774 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3775 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3776 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3777 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3778 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3779 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3780 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3781 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3782 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3783 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3784 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3785 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3786 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3787 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3788 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3789 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3790 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3791 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3792 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3793 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3794 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3795 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3796 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3797 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3798 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3799 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3800 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3801 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3802 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3803 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3804 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3805 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3806 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3807 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3808 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3809 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3810 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3811 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3812 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3813 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3814 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3815 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3816 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3817 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3818 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3819 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3820 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3821 <!-- TOPP_FileFilter_37 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3822 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3823 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3824 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3825 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3826 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3827 <param name="in" value="FileFilter_1_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3828 <output name="out" value="FileFilter_37_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3829 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3830 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3831 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3832 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3833 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3834 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3835 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3836 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3837 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3838 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3839 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3840 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3841 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3842 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3843 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3844 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3845 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3846 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3847 <param name="masstime" value="linear"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3848 <param name="lossy_mass_accuracy" value="0.0001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3849 <param name="intensity" value="slof"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3850 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3851 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3852 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3853 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3854 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3855 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3856 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3857 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3858 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3859 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3860 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3861 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3862 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3863 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3864 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3865 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3866 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3867 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3868 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3869 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3870 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3871 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3872 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3873 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3874 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3875 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3876 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3877 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3878 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3879 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3880 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3881 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3882 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3883 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3884 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3885 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3886 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3887 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3888 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3889 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3890 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3891 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3892 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3893 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3894 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3895 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3896 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3897 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3898 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3899 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3900 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3901 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3902 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3903 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3904 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3905 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3906 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3907 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3908 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3909 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3910 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3911 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3912 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3913 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3914 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3915 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3916 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3917 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3918 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3919 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3920 <!-- TOPP_FileFilter_38 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3921 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3922 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3923 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3924 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3925 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3926 <param name="in" value="FileFilter_1_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3927 <output name="out" value="FileFilter_38_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3928 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3929 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3930 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3931 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3932 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3933 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3934 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3935 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3936 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3937 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3938 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3939 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3940 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3941 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3942 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3943 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3944 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3945 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3946 <param name="masstime" value="linear"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3947 <param name="lossy_mass_accuracy" value="0.0001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3948 <param name="intensity" value="pic"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3949 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3950 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3951 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3952 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3953 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3954 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3955 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3956 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3957 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3958 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3959 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3960 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3961 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3962 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3963 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3964 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3965 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3966 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3967 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3968 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3969 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3970 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3971 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3972 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3973 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3974 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3975 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3976 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3977 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3978 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3979 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3980 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3981 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3982 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
3983 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3984 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3985 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3986 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3987 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3988 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3989 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3990 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3991 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3992 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3993 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3994 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3995 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3996 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3997 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3998 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3999 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4000 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4001 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4002 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4003 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4004 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4005 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4006 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4007 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4008 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4009 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4010 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4011 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4012 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4013 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4014 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4015 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4016 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4017 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4018 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4019 <!-- TOPP_FileFilter_40 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4020 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4021 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4022 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4023 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4024 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4025 <param name="in" value="FileFilter_40_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4026 <output name="out" value="FileFilter_40_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4027 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4028 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4029 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4030 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4031 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4032 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4033 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4034 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4035 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4036 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4037 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4038 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4039 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4040 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4041 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4042 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4043 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4044 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4045 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4046 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4047 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4048 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4049 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4050 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4051 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4052 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4053 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4054 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4055 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4056 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4057 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4058 <param name="select_polarity" value="positive"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4059 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4060 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4061 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4062 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4063 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4064 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4065 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4066 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4067 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4068 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4069 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4070 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4071 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4072 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4073 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4074 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4075 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4076 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4077 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4078 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4079 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4080 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4081 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4082 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4083 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4084 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4085 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4086 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4087 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4088 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4089 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4090 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4091 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4092 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4093 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4094 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4095 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4096 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4097 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4098 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4099 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4100 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4101 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4102 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4103 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4104 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4105 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4106 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4107 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4108 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4110 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4111 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4112 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4113 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4114 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4115 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4116 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4117 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4118 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4119 <!-- TOPP_FileFilter_41 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4120 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4121 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4122 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4123 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4124 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4125 <param name="in" value="FileFilter_40_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4126 <output name="out" value="FileFilter_41_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4127 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4128 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4129 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4130 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4131 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4132 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4133 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4134 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4135 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4136 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4137 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4138 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4139 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4140 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4141 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4142 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4143 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4144 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4145 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4146 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4147 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4148 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4149 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4150 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4151 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4152 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4153 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4154 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4155 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4156 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4157 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4158 <param name="select_polarity" value="negative"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4159 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4160 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4161 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4162 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4163 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4164 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4165 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4166 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4167 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4168 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4169 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4170 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4171 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4172 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4173 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4174 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4175 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4176 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4177 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4178 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4179 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4180 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4181 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4182 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4183 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4184 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4185 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4186 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4187 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4188 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4189 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4190 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4191 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4192 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4193 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4194 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4195 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4196 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4197 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4198 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4199 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4200 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4201 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4202 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4203 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4204 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4205 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4206 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4207 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4208 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4209 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4210 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4211 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4212 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4213 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4214 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4215 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4216 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4217 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4218 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4219 <!-- TOPP_FileFilter_42 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4220 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4221 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4222 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4223 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4224 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4225 <param name="in" value="FileFilter_40_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4226 <output name="out" value="FileFilter_42_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4227 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4228 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4229 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4230 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4231 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4232 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4233 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4234 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4235 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4236 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4237 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4238 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4239 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4240 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4241 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4242 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4243 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4244 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4245 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4246 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4247 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4248 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4249 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4250 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4251 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4252 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4253 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4254 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4255 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4256 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4257 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4258 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4259 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4260 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4261 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4262 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4263 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4264 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4265 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4266 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4267 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4268 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4269 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4270 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4271 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4272 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4273 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4274 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4275 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4276 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4277 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4278 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4279 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4280 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4281 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4282 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4283 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4284 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4285 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4286 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4287 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4288 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4289 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4290 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4291 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4292 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4293 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4294 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4295 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4296 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4297 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4298 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4299 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4300 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4301 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4302 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4303 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4304 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4305 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4306 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4307 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4308 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4309 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4310 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4311 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4312 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4313 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4314 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4315 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4316 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4317 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4318 <!-- TOPP_FileFilter_43 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4319 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4320 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4321 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4322 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4323 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4324 <param name="in" value="FileFilter_43_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4325 <output name="out" value="FileFilter_43_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4326 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4327 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4328 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4329 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4330 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4331 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4332 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4333 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4334 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4335 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4336 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4337 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4338 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4339 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4340 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4341 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4342 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4343 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4344 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4345 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4346 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4347 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4348 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4349 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4350 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4351 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4352 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4353 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4354 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4355 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4356 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4357 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4358 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4359 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4360 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4361 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4362 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4363 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4364 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4365 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4366 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4367 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4368 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4369 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4370 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4371 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4372 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4373 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4374 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4375 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4376 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4377 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4378 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4379 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4380 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4381 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4382 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4383 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4384 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4385 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4386 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4387 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4388 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4389 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4390 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4391 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4392 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4393 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4394 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4395 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4396 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4397 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4398 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4399 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4400 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4401 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4402 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4403 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4404 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4405 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4406 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4408 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4409 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4410 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4411 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4412 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4413 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4414 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4415 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4416 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4417 <!-- TOPP_FileFilter_43_read_again --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4418 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4419 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4420 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4421 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4422 </section> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4423 <param name="in" value="FileFilter_43_output.mzML"/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4424 <output name="out" value="FileFilter_43.dummy.tmp" compare="sim_size" delta_frac="0.7"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4425 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4426 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4427 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4428 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4429 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4430 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4431 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4432 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4433 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4434 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4435 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4436 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4437 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4438 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4439 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4440 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4441 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4442 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4443 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4444 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4445 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4446 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4447 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4448 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4449 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4450 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4451 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4452 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4453 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4454 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4455 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4456 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4457 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4458 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4459 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4460 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4461 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4462 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4463 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4464 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4465 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4466 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4467 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4468 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4469 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4470 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4471 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4472 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4473 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4474 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4475 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4476 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4477 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4478 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4479 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4480 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4481 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4482 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4483 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4484 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4485 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4486 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4487 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4488 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4489 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4490 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4491 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4492 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4493 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4494 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4495 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4496 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4497 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4498 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4499 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4500 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4501 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4502 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4503 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4504 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4505 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4506 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4507 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4508 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4509 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4510 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4511 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4512 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4513 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4514 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4515 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4516 <!-- TOPP_FileFilter_44 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4517 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4518 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4519 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4520 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4521 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4522 <param name="in" value="FileFilter_44_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4523 <output name="out" value="FileFilter_44_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4524 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4525 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4526 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4527 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4528 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4529 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4530 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4531 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4532 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4533 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4534 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4535 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4536 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4537 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4538 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4539 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4540 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4541 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4542 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4543 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4544 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4545 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4546 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4547 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4548 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4549 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4550 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4551 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4552 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4553 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4554 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4555 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4556 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4557 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4558 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4559 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4560 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4561 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4562 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4563 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4564 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4565 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4566 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4567 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4568 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4569 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4570 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4571 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4572 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4573 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4574 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4575 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4576 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4577 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4578 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4579 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4580 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4581 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4582 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4583 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4584 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4585 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4586 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4587 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4588 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4589 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4590 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4591 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4592 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4593 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4594 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4595 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4596 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4597 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4598 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4599 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4600 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4601 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4602 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4603 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4604 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4605 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4606 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4607 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4608 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4609 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4610 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4611 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4612 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4613 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4614 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4615 <!-- TOPP_FileFilter_45 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4616 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4617 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4618 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4619 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4620 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4621 <param name="in" value="FileFilter_45_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4622 <output name="out" value="FileFilter_45_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4623 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4624 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4625 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4626 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4627 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4628 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4629 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4630 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4631 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4632 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4633 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4634 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4635 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4636 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4637 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4638 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4639 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4640 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4641 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4642 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4643 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4644 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4645 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4646 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4647 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4648 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4649 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4650 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4651 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4652 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4653 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4654 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4655 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4656 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4657 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4658 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4659 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4660 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4661 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4662 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4663 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4664 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4665 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4666 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4667 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4668 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4669 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4670 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4671 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4672 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4673 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4674 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4675 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4676 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4677 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4678 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4679 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4680 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4681 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4682 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4683 <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4684 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4685 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4686 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4687 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4688 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4689 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4690 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4691 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4692 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4693 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4694 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4695 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4696 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4697 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4698 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4699 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4700 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4701 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4702 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4703 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4704 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4706 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4707 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4708 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4709 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4710 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4711 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4712 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4713 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4714 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4715 <!-- TOPP_FileFilter_46 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4716 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4717 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4718 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4719 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4720 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4721 <param name="in" value="FileFilter_46_input.featureXML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4722 <output name="out" value="FileFilter_46_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4723 <param name="out_type" value="featureXML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4724 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4725 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4726 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4727 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4728 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4729 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4730 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4731 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4732 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4733 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4734 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4735 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4736 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4737 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4738 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4739 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4740 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4741 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4742 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4743 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4744 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4745 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4746 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4747 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4748 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4749 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4750 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4751 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4752 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4753 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4754 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4755 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4756 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4757 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4758 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4759 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4760 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4761 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4762 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4763 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4764 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4765 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4766 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4767 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4768 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4769 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4770 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4771 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4772 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4773 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4774 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4775 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4776 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4777 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4778 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4779 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4780 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4781 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4782 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4783 <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4784 <param name="sequence_comparison_method" value="exact"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4785 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4786 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4787 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4788 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4789 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4790 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4791 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4792 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4793 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4794 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4795 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4796 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4797 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4798 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4799 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4800 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4801 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4802 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4803 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4804 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4805 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4806 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4807 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4808 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4809 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4810 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4811 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4812 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4813 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4814 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4815 <!-- TOPP_FileFilter_47 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4816 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4817 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4818 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4819 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4820 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4821 <param name="in" value="FileFilter_47_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4822 <output name="out" value="FileFilter_47_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4823 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4824 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4825 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4826 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4827 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4828 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4829 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4830 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4831 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4832 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4833 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4834 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4835 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4836 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4837 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4838 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4839 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4840 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4841 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4842 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4843 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4844 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4845 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4846 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4847 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4848 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4849 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4850 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4851 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4852 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4853 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4854 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4855 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4856 <param name="file" value="FileFilter_47_input_select.mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4857 <param name="similarity_threshold" value="0.9"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4858 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4859 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4860 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4861 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4862 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4863 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4864 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4865 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4866 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4867 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4868 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4869 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4870 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4871 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4872 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4873 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4874 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4875 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4876 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4877 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4878 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4879 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4880 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4881 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4882 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4883 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4884 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4885 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4886 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4887 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4888 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4889 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4890 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4891 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4892 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4893 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4894 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4895 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4896 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4897 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4898 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4899 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4900 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4901 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4902 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4903 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4904 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4905 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4906 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4907 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4908 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4909 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4910 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4911 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4912 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4913 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4914 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4915 <!-- TOPP_FileFilter_48 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4916 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4917 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4918 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4919 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4920 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4921 <param name="in" value="FileFilter_47_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4922 <output name="out" value="FileFilter_48_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4923 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4924 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4925 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4926 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4927 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4928 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4929 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4930 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4931 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4932 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4933 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4934 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4935 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4936 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4937 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4938 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4939 <param name="zlib_compression" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4940 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4941 <param name="masstime" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4942 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4943 <param name="intensity" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4944 <param name="float_da" value="none"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4945 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4946 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4947 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4948 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4949 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4950 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4951 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4952 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4953 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4954 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4955 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4956 <param name="file" value="FileFilter_47_input_select.mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4957 <param name="similarity_threshold" value="0.9"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4958 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4959 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4960 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4961 <param name="blacklist" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4962 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4963 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4964 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4965 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4966 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4967 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4968 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4969 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4970 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4971 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4972 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4973 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4974 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4975 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4976 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4977 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4978 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4979 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4980 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4981 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4982 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4983 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4984 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4985 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4986 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4987 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4988 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4989 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4990 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4991 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4992 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4993 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4994 <param name="max_intensity" value="-1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4995 <param name="auto_max_stdev_factor" value="3.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4996 <param name="auto_max_percentile" value="95"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4997 <param name="auto_mode" value="0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4998 <param name="win_len" value="200.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
4999 <param name="bin_count" value="30"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5000 <param name="min_required_elements" value="10"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5001 <param name="noise_for_empty_window" value="1e+20"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5002 <param name="write_log_messages" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5003 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5004 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5005 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5006 <output name="ctd_out" ftype="xml"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5007 <assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5008 <is_valid_xml/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5009 </assert_contents> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5010 </output> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
5011 <assert_stdout> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
5012 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
|
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
5013 </assert_stdout> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5014 </test> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5015 <!-- TOPP_FileFilter_49 --> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5016 <test expect_num_outputs="2"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5017 <section name="adv_opts"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5018 <param name="force" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5019 <param name="test" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5020 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5021 <param name="in" value="FileFilter_49_input.mzML"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
5022 <output name="out" value="FileFilter_49_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5023 <param name="out_type" value="mzML"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5024 <param name="rt" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5025 <param name="mz" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5026 <param name="int" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5027 <param name="sort" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5028 <section name="peak_options"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5029 <param name="sn" value="0.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5030 <param name="pc_mz_range" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5031 <param name="level" value="1 2 3"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5032 <param name="sort_peaks" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5033 <param name="no_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5034 <param name="remove_chromatograms" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5035 <param name="remove_empty" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5036 <param name="mz_precision" value="64"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5037 <param name="int_precision" value="32"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5038 <param name="indexed_file" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5039 <param name="zlib_compression" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5040 <section name="numpress"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5041 <param name="masstime" value="linear"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5042 <param name="lossy_mass_accuracy" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5043 <param name="intensity" value="pic"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5044 <param name="float_da" value="slof"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5045 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5046 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5047 <section name="spectra"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5048 <param name="remove_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5049 <param name="remove_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5050 <param name="remove_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5051 <param name="select_zoom" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5052 <param name="select_collision_energy" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5053 <param name="select_isolation_window_width" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5054 <param name="replace_pc_charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5055 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5056 <param name="similarity_threshold" value="-1.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5057 <param name="rt" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5058 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5059 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5060 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5061 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5062 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5063 <section name="feature"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5064 <param name="q" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5065 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5066 <section name="consensus"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5067 <param name="map_and" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5068 <section name="blackorwhitelist"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5069 <param name="blacklist" value="true"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5070 <param name="rt" value="60.0"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5071 <param name="mz" value="0.01"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5072 <param name="use_ppm_tolerance" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5073 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5074 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5075 <section name="f_and_c"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5076 <param name="charge" value=":"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5077 <param name="size" value=":"/> |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
5078 <param name="remove_hull" value="false"/> |
|
15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5079 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5080 <section name="id"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5081 <param name="remove_clashes" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5082 <param name="keep_best_score_id" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5083 <param name="sequence_comparison_method" value="substring"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5084 <param name="remove_annotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5085 <param name="remove_unannotated_features" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5086 <param name="remove_unassigned_ids" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5087 <param name="rt" value="0.1"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5088 <param name="mz" value="0.001"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5089 <param name="blacklist_imperfect" value="false"/> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5090 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5091 <section name="algorithm"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
5092 <section name="SignalToNoise"> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5093 <param name="max_intensity" value="-1"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5094 <param name="auto_max_stdev_factor" value="3.0"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5095 <param name="auto_max_percentile" value="95"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5096 <param name="auto_mode" value="0"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5097 <param name="win_len" value="200.0"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5098 <param name="bin_count" value="30"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
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5099 <param name="min_required_elements" value="10"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5100 <param name="noise_for_empty_window" value="1e+20"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5101 <param name="write_log_messages" value="true"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5102 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5103 </section> |
|
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5104 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5105 <output name="ctd_out" ftype="xml"> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5106 <assert_contents> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5107 <is_valid_xml/> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5108 </assert_contents> |
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fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5109 </output> |
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16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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5110 <assert_stdout> |
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86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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5111 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
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86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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5112 </assert_stdout> |
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15
fe4e4587d265
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5113 </test> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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5114 </tests> |
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acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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5115 <help><![CDATA[Extracts or manipulates portions of data from peak, feature or consensus-feature files. |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5116 |
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fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff
changeset
|
5117 |
|
16
86a9dd43dd09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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5118 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileFilter.html]]></help> |
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11
acf2b5b25c75
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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5119 <expand macro="references"/> |
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0
fa19593551c6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5120 </tool> |