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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ProteinInference" name="ProteinInference" version="2.0.0">
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3 <description>Protein inference based on the number of identified peptides.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ProteinInference</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>ProteinInference
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_min_peptides_per_protein:
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19 -min_peptides_per_protein $param_min_peptides_per_protein
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20 #end if
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21 #if $param_treat_charge_variants_separately:
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22 -treat_charge_variants_separately
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23 #end if
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24 #if $param_treat_modification_variants_separately:
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25 -treat_modification_variants_separately
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
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28 #if $adv_opts.adv_opts_selector=='advanced':
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29 #if $adv_opts.param_force:
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30 -force
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31 #end if
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32 #end if
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33 </command>
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34 <inputs>
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35 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
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36 <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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37 <param name="param_treat_charge_variants_separately" 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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38 <param name="param_treat_modification_variants_separately" 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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39 <expand macro="advanced_options">
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40 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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41 </expand>
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42 </inputs>
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43 <outputs>
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44 <data name="param_out" format="idxml"/>
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45 </outputs>
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46 <help>**What it does**
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47
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48 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 <expand macro="references"/>
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53 </tool>
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