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annotate ProteinInference.xml @ 4:8131d9872095 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author galaxyp
date Thu, 11 Jan 2018 18:05:56 -0500
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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: [Identification]-->
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4 <tool id="ProteinInference" name="ProteinInference" version="2.2.0">
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5 <description>Protein inference based on the number of identified peptides.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ProteinInference</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>ProteinInference
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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_min_peptides_per_protein:
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22 -min_peptides_per_protein $param_min_peptides_per_protein
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23 #end if
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24 #if $param_treat_charge_variants_separately:
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25 -treat_charge_variants_separately
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26 #end if
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27 #if $param_treat_modification_variants_separately:
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28 -treat_modification_variants_separately
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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_min_peptides_per_protein" type="integer" min="1" optional="True" value="2" label="Minimal number of peptides needed for a protein identification" help="(-min_peptides_per_protein) "/>
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39 <param name="param_treat_charge_variants_separately" display="radio" type="boolean" truevalue="-treat_charge_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" help="(-treat_charge_variants_separately) "/>
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40 <param name="param_treat_modification_variants_separately" display="radio" type="boolean" truevalue="-treat_modification_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" help="(-treat_modification_variants_separately) "/>
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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>Protein inference based on the number of identified peptides.
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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/TOPP_ProteinInference.html</help>
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52 </tool>