Mercurial > repos > galaxyp > openms_featurelinkerunlabeledkd
annotate FeatureLinkerUnlabeledKD.xml @ 10:7a9d97cfe93c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:40:20 +0000 |
| parents | 2570414d1fd9 |
| children | 718c0e2904cb |
| rev | line source |
|---|---|
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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1 <?xml version='1.0' encoding='UTF-8'?> |
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4
17aa0e144300
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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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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3 <!--Proposed Tool Section: [Map Alignment]--> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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4 <tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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5 <description>Groups corresponding features from multiple maps.</description> |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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6 <macros> |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token> |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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8 <import>macros.xml</import> |
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8
2570414d1fd9
"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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2570414d1fd9
"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
b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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11 </macros> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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12 <expand macro="requirements"/> |
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0
b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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13 <expand macro="stdio"/> |
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2570414d1fd9
"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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2570414d1fd9
"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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2570414d1fd9
"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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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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17 |
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2570414d1fd9
"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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2570414d1fd9
"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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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } |
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2570414d1fd9
"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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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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22 #if $design: |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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23 mkdir design && |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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24 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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25 #end if |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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26 |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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27 ## Main program call |
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2570414d1fd9
"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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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 set -o pipefail && |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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30 @EXECUTABLE@ -write_ctd ./ && |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 -in |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 -out |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 'out/output.${gxy2omsext("consensusxml")}' |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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37 #if $design: |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 -design |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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40 #end if |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 ## Postprocessing |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out' |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 #end if]]></command> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 <configfiles> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 <inputs name="args_json" data_style="paths"/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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50 </configfiles> |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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51 <inputs> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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52 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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53 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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54 <param name="keep_subelements" argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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55 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 <param name="mz_unit" argument="-algorithm:mz_unit" display="radio" type="select" optional="false" label="Unit of m/z tolerance" help=""> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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57 <option value="ppm" selected="true">ppm</option> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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58 <option value="Da">Da</option> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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59 <expand macro="list_string_san"/> |
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b73b578a6c11
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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60 </param> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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61 <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="Number of partitions in m/z space" help=""/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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62 <section name="warp" title="" help="" expanded="false"> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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63 <param name="enabled" argument="-algorithm:warp:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help=""/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 <param name="rt_tol" argument="-algorithm:warp:rt_tol" type="float" optional="true" min="0.0" value="100.0" label="Width of RT tolerance window (sec)" help=""/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65 <param name="mz_tol" argument="-algorithm:warp:mz_tol" type="float" optional="true" min="0.0" value="5.0" label="m/z tolerance (in ppm or Da)" help=""/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 <param name="max_pairwise_log_fc" argument="-algorithm:warp:max_pairwise_log_fc" type="float" optional="true" value="0.5" label="Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value < 0 disables the FC check"/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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67 <param name="min_rel_cc_size" argument="-algorithm:warp:min_rel_cc_size" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help=""/> |
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2570414d1fd9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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68 <param name="max_nr_conflicts" argument="-algorithm:warp:max_nr_conflicts" type="integer" optional="true" min="-1" value="0" label="Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help=""/> |
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2570414d1fd9
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69 </section> |
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70 <section name="link" title="" help="" expanded="false"> |
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71 <param name="rt_tol" argument="-algorithm:link:rt_tol" type="float" optional="true" min="0.0" value="30.0" label="Width of RT tolerance window (sec)" help=""/> |
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72 <param name="mz_tol" argument="-algorithm:link:mz_tol" type="float" optional="true" min="0.0" value="10.0" label="m/z tolerance (in ppm or Da)" help=""/> |
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73 <param name="charge_merging" argument="-algorithm:link:charge_merging" display="radio" type="select" optional="false" label="whether to disallow charge mismatches (Identical), allow to link charge zero" help="(i.e., unknown charge state) with every charge state, or disregard charges (Any)"> |
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74 <option value="Identical">Identical</option> |
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75 <option value="With_charge_zero" selected="true">With_charge_zero</option> |
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76 <option value="Any">Any</option> |
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77 <expand macro="list_string_san"/> |
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78 </param> |
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79 <param name="adduct_merging" argument="-algorithm:link:adduct_merging" display="radio" type="select" optional="false" label="whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any)" help=""> |
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80 <option value="Identical">Identical</option> |
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81 <option value="With_unknown_adducts">With_unknown_adducts</option> |
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82 <option value="Any" selected="true">Any</option> |
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83 <expand macro="list_string_san"/> |
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84 </param> |
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85 </section> |
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86 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false"> |
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87 <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> |
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88 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/> |
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89 </section> |
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90 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false"> |
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91 <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> |
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92 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/> |
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93 </section> |
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94 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false"> |
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95 <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> |
|
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96 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="1.0" label="Final intensity distances are weighted by this facto" help=""/> |
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97 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> |
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98 <option value="enabled" selected="true">enabled</option> |
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99 <option value="disabled">disabled</option> |
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100 <expand macro="list_string_san"/> |
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101 </param> |
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102 </section> |
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103 <section name="LOWESS" title="LOWESS parameters for internal RT transformations (only relevant if 'warp:enabled' is set to 'true')" help="" expanded="false"> |
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104 <param name="span" argument="-algorithm:LOWESS:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/> |
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105 <param name="num_iterations" argument="-algorithm:LOWESS:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/> |
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106 <param name="delta" argument="-algorithm:LOWESS:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/> |
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107 <param name="interpolation_type" argument="-algorithm:LOWESS:interpolation_type" display="radio" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation"> |
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108 <option value="linear">linear</option> |
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109 <option value="cspline" selected="true">cspline</option> |
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110 <option value="akima">akima</option> |
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111 <expand macro="list_string_san"/> |
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112 </param> |
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113 <param name="extrapolation_type" argument="-algorithm:LOWESS:extrapolation_type" display="radio" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation"> |
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114 <option value="two-point-linear">two-point-linear</option> |
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115 <option value="four-point-linear" selected="true">four-point-linear</option> |
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116 <option value="global-linear">global-linear</option> |
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117 <expand macro="list_string_san"/> |
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118 </param> |
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119 </section> |
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120 </section> |
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121 <expand macro="adv_opts_macro"> |
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10
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122 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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8
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123 <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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124 <expand macro="list_string_san"/> |
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0
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125 </param> |
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126 </expand> |
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10
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127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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8
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128 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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129 </param> |
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0
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130 </inputs> |
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131 <outputs> |
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8
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132 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> |
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133 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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134 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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135 </data> |
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136 </outputs> |
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137 <tests> |
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138 <expand macro="autotest_FeatureLinkerUnlabeledKD"/> |
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139 <expand macro="manutest_FeatureLinkerUnlabeledKD"/> |
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140 </tests> |
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141 <help><![CDATA[Groups corresponding features from multiple maps. |
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142 |
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143 |
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144 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureLinkerUnlabeledKD.html]]></help> |
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145 <expand macro="references"/> |
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146 </tool> |