Mercurial > repos > galaxyp > openms_idextractor

annotate IDExtractor.xml @ 4:472809ff333b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:45:11 -0400
parents 20d8fceb0c05
children b18310842a0a
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f42812df11d8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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: [Utilities]-->
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4 <tool id="IDExtractor" name="IDExtractor" version="2.2.0">
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5 <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDExtractor</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>IDExtractor
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_number_of_peptides:
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22 -number_of_peptides $param_number_of_peptides
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23 #end if
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24 #if $param_number_of_rand_invokations:
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25 -number_of_rand_invokations $param_number_of_rand_invokations
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26 #end if
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27 #if $param_best_hits:
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28 -best_hits
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29 #end if
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30 #if $adv_opts.adv_opts_selector=='advanced':
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31 #if $adv_opts.param_force:
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32 -force
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33 #end if
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34 #end if
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35 </command>
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36 <inputs>
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37 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
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38 <param name="param_number_of_peptides" type="integer" min="1" optional="True" value="10" label="Number of randomly chosen peptides" help="(-number_of_peptides) "/>
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39 <param name="param_number_of_rand_invokations" type="integer" min="0" optional="True" value="0" label="Number of rand invocations before random draw" help="(-number_of_rand_invokations) "/>
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40 <param name="param_best_hits" display="radio" type="boolean" truevalue="-best_hits" falsevalue="" checked="false" optional="True" label="If this flag is set the best n peptides are chosen" help="(-best_hits) "/>
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41 <expand macro="advanced_options">
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42 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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43 </expand>
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44 </inputs>
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45 <outputs>
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46 <data name="param_out" format="idxml"/>
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47 </outputs>
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48 <help>Extracts 'n' peptides randomly or best 'n' from idXML files.
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49
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50
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51 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDExtractor.html</help>
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52 </tool>