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annotate OpenSwathFeatureXMLToTSV.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: [Targeted Experiments]-->
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4 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.0.0">
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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 $param_best_scoring_peptide:
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29 -best_scoring_peptide &quot;$param_best_scoring_peptide&quot;
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30 #end if
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31 -threads \${GALAXY_SLOTS:-24}
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32 #if $adv_opts.adv_opts_selector=='advanced':
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33 #if $adv_opts.param_force:
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34 -force
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35 #end if
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36 #end if
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37 </command>
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38 <inputs>
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39 <param format="xml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="'"/>
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43 <remove value="&quot;"/>
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44 </valid>
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45 </sanitizer>
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46 </param>
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47 <param format="traml" help="(-tr) " label="TraML transition file" name="param_tr" optional="False" type="data"/>
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48 <param checked="false" falsevalue="" help="(-short_format) " label="Whether to write short (one peptide per line) or long format (one transition per line)" name="param_short_format" optional="True" truevalue="-short_format" type="boolean"/>
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49 <param help="(-best_scoring_peptide) " label="If only the best scoring feature per peptide should be printed, give the variable name" name="param_best_scoring_peptide" size="30" type="text">
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50 <sanitizer>
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51 <valid initial="string.printable">
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52 <remove value="'"/>
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53 <remove value="&quot;"/>
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54 </valid>
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55 </sanitizer>
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56 </param>
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57 <expand macro="advanced_options">
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58 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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59 </expand>
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60 </inputs>
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61 <outputs>
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62 <data format="tabular" name="param_out"/>
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63 </outputs>
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64 <help>Converts a featureXML to a mProphet tsv.
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65
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66
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67 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
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68 </tool>