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annotate IDMerger.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="IDMerger" name="IDMerger" version="2.0.0">
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5 <description>Merges several protein/peptide identification files into one file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDMerger</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>IDMerger
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14
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15 -in
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16 $param_in1
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17 #for $infile in $inputs
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18 $infile.param_in
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19 #end for
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20 -out $param_out
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21 #if $param_add_to:
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22 -add_to $param_add_to
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23 #end if
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24 #if $param_annotate_file_origin:
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25 -annotate_file_origin
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26 #end if
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27 #if $param_pepxml_protxml:
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28 -pepxml_protxml
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29 #end if
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30 -threads \${GALAXY_SLOTS:-24}
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31 #if $adv_opts.adv_opts_selector=='advanced':
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32 #if $adv_opts.param_force:
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33 -force
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34 #end if
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35 #end if
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36 </command>
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37 <inputs>
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38 <param name="param_in1" type="data" format="idxml" label="Input files" help="(-in)" />
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39 <repeat name="inputs" title="Input files">
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40 <param name="param_in" type="data" format="idxml" label="Input files" help="(-in)" />
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41 </repeat>
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42
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43 <param format="xml" help="(-add_to) IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)" label="Optional input file" name="param_add_to" optional="True" type="data"/>
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44 <param checked="false" falsevalue="" help="(-annotate_file_origin) " label="Store the original filename in each protein/peptide identification (meta value: file_origin)" name="param_annotate_file_origin" optional="True" truevalue="-annotate_file_origin" type="boolean"/>
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45 <param checked="false" falsevalue="" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'" label="Merge idXML files derived from a pepXML and corresponding protXML file" name="param_pepxml_protxml" optional="True" truevalue="-pepxml_protxml" type="boolean"/>
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46 <expand macro="advanced_options">
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47 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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48 </expand>
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49 </inputs>
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50 <outputs>
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51 <data format="xml" name="param_out"/>
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52 </outputs>
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53 <help>Merges several protein/peptide identification files into one file.
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54
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56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html</help>
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57 </tool>