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comparison ProteinInference.xml @ 0:53c4762b5c8c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:46:36 -0500
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children 7162baa3ac58
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-1:000000000000 0:53c4762b5c8c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="ProteinInference" name="ProteinInference" version="2.1.0">
5 <description>Protein inference based on the number of identified peptides.</description>
6 <macros>
7 <token name="@EXECUTABLE@">ProteinInference</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ProteinInference
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_min_peptides_per_protein:
22 -min_peptides_per_protein $param_min_peptides_per_protein
23 #end if
24 #if $param_treat_charge_variants_separately:
25 -treat_charge_variants_separately
26 #end if
27 #if $param_treat_modification_variants_separately:
28 -treat_modification_variants_separately
29 #end if
30 #if $adv_opts.adv_opts_selector=='advanced':
31 #if $adv_opts.param_force:
32 -force
33 #end if
34 #end if
35 </command>
36 <inputs>
37 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
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) "/>
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) "/>
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) "/>
41 <expand macro="advanced_options">
42 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
43 </expand>
44 </inputs>
45 <outputs>
46 <data name="param_out" format="idxml"/>
47 </outputs>
48 <help>Protein inference based on the number of identified peptides.
49
50
51 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html</help>
52 </tool>