Mercurial > repos > galaxyp > openms_tofcalibration
annotate TOFCalibration.xml @ 12:cfd9c633de6b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
| author | galaxyp |
|---|---|
| date | Fri, 06 Nov 2020 19:48:41 +0000 |
| parents | 90f459a4da0e |
| children | 9f0e189d093c |
| rev | line source |
|---|---|
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5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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1 <?xml version='1.0' encoding='UTF-8'?> |
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5
0ca1ea28f6ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--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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5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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4 <tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
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0
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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5 <description>Applies time of flight calibration.</description> |
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5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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6 <macros> |
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5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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7 <token name="@EXECUTABLE@">TOFCalibration</token> |
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5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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8 <import>macros.xml</import> |
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9
40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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9 <import>macros_autotest.xml</import> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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10 <import>macros_test.xml</import> |
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0
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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11 </macros> |
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9
40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 <expand macro="requirements"/> |
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0
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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13 <expand macro="stdio"/> |
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9
40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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15 @EXT_FOO@ |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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16 #import re |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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17 |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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18 ## Preprocessing |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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19 mkdir in && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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21 mkdir out && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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22 mkdir ext_calibrants && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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23 ln -s '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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24 mkdir ref_masses && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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25 ln -s '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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26 mkdir tof_const && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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27 ln -s '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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28 |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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29 ## Main program call |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 set -o pipefail && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 @EXECUTABLE@ -write_ctd ./ && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 -in |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 -out |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 'out/output.${gxy2omsext("mzml")}' |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 -ext_calibrants |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 -ref_masses |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 -tof_const |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' |
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5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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45 |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 ## Postprocessing |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 && mv 'out/output.${gxy2omsext("mzml")}' '$out' |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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50 #end if]]></command> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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51 <configfiles> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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52 <inputs name="args_json" data_style="paths"/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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54 </configfiles> |
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0
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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55 <inputs> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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57 <param name="ext_calibrants" argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/> |
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90f459a4da0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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58 <param name="ref_masses" argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/> |
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90f459a4da0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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59 <param name="tof_const" argument="-tof_const" type="data" format="tabular" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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60 <param name="peak_data" argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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61 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false"> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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62 <section name="PeakPicker" title="" help="" expanded="false"> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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63 <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65 <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 <param name="estimate_peak_width" argument="-algorithm:PeakPicker:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/> |
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40a101cabd0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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67 <param name="fwhm_lower_bound_factor" argument="-algorithm:PeakPicker:fwhm_lower_bound_factor" type="float" optional="true" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/> |
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68 <param name="fwhm_upper_bound_factor" argument="-algorithm:PeakPicker:fwhm_upper_bound_factor" type="float" optional="true" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/> |
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69 <section name="optimization" title="" help="" expanded="false"> |
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70 <param name="iterations" argument="-algorithm:PeakPicker:optimization:iterations" type="integer" optional="true" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/> |
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71 <section name="penalties" title="" help="" expanded="false"> |
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72 <param name="position" argument="-algorithm:PeakPicker:optimization:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/> |
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73 <param name="left_width" argument="-algorithm:PeakPicker:optimization:penalties:left_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/> |
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74 <param name="right_width" argument="-algorithm:PeakPicker:optimization:penalties:right_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/> |
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75 <param name="height" argument="-algorithm:PeakPicker:optimization:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/> |
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76 </section> |
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77 <section name="2d" title="" help="" expanded="false"> |
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78 <param name="tolerance_mz" argument="-algorithm:PeakPicker:optimization:2d:tolerance_mz" type="float" optional="true" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/> |
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79 <param name="max_peak_distance" argument="-algorithm:PeakPicker:optimization:2d:max_peak_distance" type="float" optional="true" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/> |
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80 </section> |
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81 </section> |
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82 <section name="thresholds" title="" help="" expanded="false"> |
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83 <param name="peak_bound" argument="-algorithm:PeakPicker:thresholds:peak_bound" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity" help=""/> |
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84 <param name="peak_bound_ms2_level" argument="-algorithm:PeakPicker:thresholds:peak_bound_ms2_level" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/> |
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85 <param name="correlation" argument="-algorithm:PeakPicker:thresholds:correlation" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/> |
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86 <param name="noise_level" argument="-algorithm:PeakPicker:thresholds:noise_level" type="float" optional="true" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/> |
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87 <param name="search_radius" argument="-algorithm:PeakPicker:thresholds:search_radius" type="integer" optional="true" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/> |
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88 </section> |
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89 <section name="wavelet_transform" title="" help="" expanded="false"> |
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90 <param name="spacing" argument="-algorithm:PeakPicker:wavelet_transform:spacing" type="float" optional="true" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/> |
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91 </section> |
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92 <section name="deconvolution" title="" help="" expanded="false"> |
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93 <param name="deconvolution" argument="-algorithm:PeakPicker:deconvolution:deconvolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If you want heavily overlapping peaks to be separated set this value to "true"" help=""/> |
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94 <param name="asym_threshold" argument="-algorithm:PeakPicker:deconvolution:asym_threshold" type="float" optional="true" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/> |
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95 <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:left_width" type="float" optional="true" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/> |
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96 <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:right_width" type="float" optional="true" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/> |
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97 <param name="scaling" argument="-algorithm:PeakPicker:deconvolution:scaling" type="float" optional="true" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/> |
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98 <section name="fitting" title="" help="" expanded="false"> |
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99 <param name="fwhm_threshold" argument="-algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold" type="float" optional="true" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/> |
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100 <param name="eps_abs" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_abs" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/> |
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101 <param name="eps_rel" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_rel" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/> |
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102 <param name="max_iteration" argument="-algorithm:PeakPicker:deconvolution:fitting:max_iteration" type="integer" optional="true" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/> |
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103 <section name="penalties" title="" help="" expanded="false"> |
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104 <param name="position" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/> |
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105 <param name="height" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/> |
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106 <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:left_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/> |
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107 <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:right_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/> |
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108 </section> |
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109 </section> |
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110 </section> |
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111 <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false"> |
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112 <param name="max_intensity" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity" type="integer" optional="true" 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 not be added to the histogram. 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)"/> |
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113 <param name="auto_max_stdev_factor" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" optional="true" 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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114 <param name="auto_max_percentile" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" optional="true" 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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115 <param name="auto_mode" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode" type="integer" optional="true" 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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116 <param name="win_len" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/> |
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117 <param name="bin_count" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/> |
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118 <param name="stdev_mp" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp" type="float" optional="true" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/> |
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119 <param name="min_required_elements" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/> |
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120 <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> |
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121 </section> |
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122 </section> |
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123 </section> |
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124 <expand macro="adv_opts_macro"> |
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125 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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126 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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127 <expand macro="list_string_san"/> |
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128 </param> |
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129 </expand> |
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130 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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132 </param> |
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133 </inputs> |
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134 <outputs> |
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135 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
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136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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138 </data> |
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139 </outputs> |
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140 <tests> |
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141 <expand macro="autotest_TOFCalibration"/> |
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142 <expand macro="manutest_TOFCalibration"/> |
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143 </tests> |
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144 <help><![CDATA[Applies time of flight calibration. |
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145 |
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146 |
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147 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_TOFCalibration.html]]></help> |
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148 <expand macro="references"/> |
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149 </tool> |