Mercurial > repos > galaxyp > openms_openswathfeaturexmltotsv

annotate OpenSwathFeatureXMLToTSV.xml @ 1:7c2109632714 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:45:52 -0400
parents 0a6de13f7148
children 4a8beda5f2dd
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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: [Targeted Experiments]-->
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4 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.1.0">
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5 <description>Converts a featureXML to a mProphet tsv.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</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>OpenSwathFeatureXMLToTSV
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14
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_tr:
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20 -tr $param_tr
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21 #end if
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22 #if $param_out:
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23 -out $param_out
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24 #end if
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25 #if $param_short_format:
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26 -short_format
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27 #end if
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28 #if $param_best_scoring_peptide:
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29 -best_scoring_peptide "$param_best_scoring_peptide"
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30 #end if
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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_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
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39 <sanitizer>
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40 <valid initial="string.printable">
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41 <remove value="'"/>
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42 <remove value="&quot;"/>
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43 </valid>
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44 </sanitizer>
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45 </param>
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46 <param name="param_tr" type="data" format="traml" optional="False" label="TraML transition file" help="(-tr) "/>
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47 <param name="param_short_format" display="radio" type="boolean" truevalue="-short_format" falsevalue="" checked="false" optional="True" label="Whether to write short (one peptide per line) or long format (one transition per line)" help="(-short_format) "/>
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48 <param name="param_best_scoring_peptide" type="text" size="30" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide) ">
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49 <sanitizer>
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50 <valid initial="string.printable">
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51 <remove value="'"/>
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52 <remove value="&quot;"/>
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53 </valid>
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54 </sanitizer>
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55 </param>
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56 <expand macro="advanced_options">
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57 <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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58 </expand>
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59 </inputs>
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60 <outputs>
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61 <data name="param_out" format="tabular"/>
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62 </outputs>
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63 <help>Converts a featureXML to a mProphet tsv.
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64
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65
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66 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
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67 </tool>