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comparison ProteinInference.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="ProteinInference" name="ProteinInference" version="1.12.0">
3 <description>Protein inference based on the number of identified peptides.</description>
4 <macros>
5 <token name="@EXECUTABLE@">ProteinInference</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>ProteinInference
11
12 -in ${param_in}
13 -out ${param_out}
14 -min_peptides_per_protein ${param_min_peptides_per_protein}
15 ${param_treat_charge_variants_separately}
16 ${param_treat_modification_variants_separately}
17 -threads \${GALAXY_SLOTS:-24}
18 </command>
19 <inputs>
20 <param name="param_in" type="data" format="idXML" optional="False" label="input file" help="(-in)"/>
21 <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)"/>
22 <param name="param_treat_charge_variants_separately" type="boolean" truevalue="-treat_charge_variants_separately true" falsevalue="-treat_charge_variants_separately false" 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)"/>
23 <param name="param_treat_modification_variants_separately" type="boolean" truevalue="-treat_modification_variants_separately true" falsevalue="-treat_modification_variants_separately false" 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)"/>
24 </inputs>
25 <outputs>
26 <data name="param_out" label="output file" format="idXML"/>
27 </outputs>
28 <help>**What it does**
29
30 Protein inference based on the number of identified peptides.
31
32
33 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html
34
35 @REFERENCES@
36 </help>
37 </tool>