Mercurial > repos > galaxyp > openms_proteininference
view ProteinInference.xml @ 7:4a39dd3bbe69 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
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date | Wed, 15 May 2019 08:07:59 -0400 |
parents | 4ffcfff137d6 |
children | e18096659b38 |
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<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Identification]--> <tool id="ProteinInference" name="ProteinInference" version="2.3.0"> <description>Protein inference based on the number of identified peptides.</description> <macros> <token name="@EXECUTABLE@">ProteinInference</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ProteinInference #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_min_peptides_per_protein: -min_peptides_per_protein $param_min_peptides_per_protein #end if #if $param_treat_charge_variants_separately: -treat_charge_variants_separately #end if #if $param_treat_modification_variants_separately: -treat_modification_variants_separately #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if ]]></command> <inputs> <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> <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) "/> <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) "/> <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) "/> <expand macro="advanced_options"> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs> <outputs> <data name="param_out" format="idxml"/> </outputs> <help>Protein inference based on the number of identified peptides. For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinInference.html</help> </tool>