Mercurial > repos > bgruening > openms
diff ProteinResolver.xml @ 4:6ead64a594bd draft default tip
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 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ProteinResolver.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,135 @@ +<?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 CTD2Galaxy.--> + <!--Proposed Tool Section: [Quantitation]--> + <tool id="ProteinResolver" name="ProteinResolver" version="2.0.0"> + <description>protein inference</description> + <macros> + <token name="@EXECUTABLE@">ProteinResolver</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>ProteinResolver + +#if $param_fasta: + -fasta $param_fasta +#end if +-in + #for token in $param_in: + $token + #end for +#if $param_in_path: + -in_path "$param_in_path" +#end if +#if $param_design: + -design $param_design +#end if +#if $param_protein_groups: + -protein_groups $param_protein_groups +#end if +#if $param_peptide_table: + -peptide_table $param_peptide_table +#end if +#if $param_protein_table: + -protein_table $param_protein_table +#end if +#if $param_additional_info: + -additional_info $param_additional_info +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_resolver_missed_cleavages: + -resolver:missed_cleavages $param_resolver_missed_cleavages +#end if +#if $param_resolver_min_length: + -resolver:min_length $param_resolver_min_length +#end if +#if $param_resolver_enzyme: + -resolver:enzyme "$param_resolver_enzyme" +#end if +#if $param_designer_experiment: + -designer:experiment "$param_designer_experiment" +#end if +#if $param_designer_file: + -designer:file "$param_designer_file" +#end if +#if $param_designer_separator: + -designer:separator + #if " " in str($param_designer_separator): + "$param_designer_separator" + #else + $param_designer_separator + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +</command> + <inputs> + <param format="fasta" help="(-fasta) " label="Input database file" name="param_fasta" optional="False" type="data"/> + <param format="xml,consensusxml" help="(-in) " label="Input file(s) holding experimental data" multiple="true" name="param_in" optional="True" size="30" type="data"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-in_path) Ignored if 'in' is given" label="Path to idXMLs or consensusXMLs files" name="param_in_path" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param format="txt" help="(-design) See documentation for specific format requirements" label="Text file containing the experimental design" name="param_design" optional="True" type="data"/> + <param help="(-missed_cleavages) " label="Number of allowed missed cleavages" min="0" name="param_resolver_missed_cleavages" optional="True" type="integer" value="2"/> + <param help="(-min_length) " label="Minimum length of peptide" min="1" name="param_resolver_min_length" optional="True" type="integer" value="6"/> + <param help="(-enzyme) " label="Digestion enzyme" name="param_resolver_enzyme" size="30" type="text" value="Trypsin"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-experiment) " label="Identifier for the experimental design" name="param_designer_experiment" size="30" type="text" value="ExperimentalSetting"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-file) " label="Identifier for the file name" name="param_designer_file" size="30" type="text" value="File"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-separator) " label="Separator, which should be used to split a row into columns" name="param_designer_separator" optional="True" type="select" value="tab"> + <option value="tab">tab</option> + <option value="semi-colon">semi-colon</option> + <option value="comma">comma</option> + <option value="whitespace">whitespace</option> + </param> + <expand macro="advanced_options"> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + </expand> + </inputs> + <outputs> + <data format="tabular" name="param_protein_groups"/> + <data format="tabular" name="param_peptide_table"/> + <data format="tabular" name="param_protein_table"/> + <data format="tabular" name="param_additional_info"/> + </outputs> + <help>protein inference + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html</help> + </tool>