Mercurial > repos > galaxyp > openms_proteininference

comparison ProteinInference.xml @ 12:aea8369cb790 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 05:22:08 -0400
parents 538e91939786
children eb639004ea27
comparison
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11:756772171e4c 12:aea8369cb790
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="ProteinInference" name="ProteinInference" version="2.2.0"> 4 <tool id="ProteinInference" name="ProteinInference" version="2.3.0">
5 <description>Protein inference based on the number of identified peptides.</description> 5 <description>Protein inference based on the number of identified peptides.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ProteinInference</token> 7 <token name="@EXECUTABLE@">ProteinInference</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>ProteinInference 13 <command detect_errors="aggressive"><![CDATA[ProteinInference
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
30 #if $adv_opts.adv_opts_selector=='advanced': 30 #if $adv_opts.adv_opts_selector=='advanced':
31 #if $adv_opts.param_force: 31 #if $adv_opts.param_force:
32 -force 32 -force
33 #end if 33 #end if
34 #end if 34 #end if
35 </command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> 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) "/> 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) "/> 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) "/> 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) "/>
46 <data name="param_out" format="idxml"/> 46 <data name="param_out" format="idxml"/>
47 </outputs> 47 </outputs>
48 <help>Protein inference based on the number of identified peptides. 48 <help>Protein inference based on the number of identified peptides.
49 49
50 50
51 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html</help> 51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinInference.html</help>
52 </tool> 52 </tool>