Mercurial > repos > galaxyp > openms_seedlistgenerator

annotate SeedListGenerator.xml @ 0:75d6ffd2afb7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 07:00:28 -0400
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75d6ffd2afb7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="SeedListGenerator" name="SeedListGenerator" version="2.3.0">
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5 <description>Generates seed lists for feature detection.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SeedListGenerator</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 detect_errors="aggressive"><![CDATA[SeedListGenerator
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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
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19 #if $rep_param_out:
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20 -out
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21 #for token in $rep_param_out:
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22 #if " " in str(token):
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23 "$token.param_out"
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24 #else
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25 $token.param_out
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26 #end if
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27 #end for
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28 #end if
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29 #if $param_use_peptide_mass:
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30 -use_peptide_mass
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31 #end if
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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 name="param_in" type="data" format="mzml,idxml,featurexml,consensusxml" optional="False" label="Input file (see below for details)" help="(-in) "/>
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40 <param name="param_use_peptide_mass" display="radio" type="boolean" truevalue="-use_peptide_mass" falsevalue="" checked="false" optional="True" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help="(-use_peptide_mass) "/>
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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="featurexml"/>
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47 </outputs>
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48 <help>Generates seed lists for feature detection.
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49
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50
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51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_SeedListGenerator.html</help>
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52 </tool>