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comparison ProteinInference.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="ProteinInference" name="ProteinInference" version="1.12.0"> 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 <description>Protein inference based on the number of identified peptides.</description> 3 <!--Proposed Tool Section: [Identification]-->
4 <macros> 4 <tool id="ProteinInference" name="ProteinInference" version="2.0.0">
5 <token name="@EXECUTABLE@">ProteinInference</token> 5 <description>Protein inference based on the number of identified peptides.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">ProteinInference</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>ProteinInference 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ProteinInference
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -min_peptides_per_protein ${param_min_peptides_per_protein} 17 #end if
15 ${param_treat_charge_variants_separately} 18 #if $param_out:
16 ${param_treat_modification_variants_separately} 19 -out $param_out
17 -threads \${GALAXY_SLOTS:-24} 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 -threads \${GALAXY_SLOTS:-24}
31 #if $adv_opts.adv_opts_selector=='advanced':
32 #if $adv_opts.param_force:
33 -force
34 #end if
35 #end if
18 </command> 36 </command>
19 <inputs> 37 <inputs>
20 <param name="param_in" type="data" format="idXML" optional="False" label="input file" help="(-in)"/> 38 <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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)"/> 39 <param help="(-min_peptides_per_protein) " label="Minimal number of peptides needed for a protein identification" min="1" name="param_min_peptides_per_protein" optional="True" type="integer" value="2"/>
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)"/> 40 <param checked="false" falsevalue="" help="(-treat_charge_variants_separately) " label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" name="param_treat_charge_variants_separately" optional="True" truevalue="-treat_charge_variants_separately" type="boolean"/>
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)"/> 41 <param checked="false" falsevalue="" help="(-treat_modification_variants_separately) " label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" name="param_treat_modification_variants_separately" optional="True" truevalue="-treat_modification_variants_separately" type="boolean"/>
24 </inputs> 42 <expand macro="advanced_options">
25 <outputs> 43 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
26 <data name="param_out" label="output file" format="idXML"/> 44 </expand>
27 </outputs> 45 </inputs>
28 <help>**What it does** 46 <outputs>
29 47 <data format="xml" name="param_out"/>
30 Protein inference based on the number of identified peptides. 48 </outputs>
49 <help>Protein inference based on the number of identified peptides.
31 50
32 51
33 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html 52 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html</help>
34 53 </tool>
35 @REFERENCES@
36 </help>
37 </tool>