Mercurial > repos > galaxyp > openms_openpepxl

comparison OpenPepXL.xml @ 2:ec2524b5a07a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Fri, 17 May 2019 05:01:49 -0400
parents f333faf508bb
children a2a842b00f9c
comparison
equal deleted inserted replaced
1:dde913004c8a 2:ec2524b5a07a
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>OpenPepXL 13 <command detect_errors="aggressive"><![CDATA[OpenPepXL
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_consensus: 18 #if $param_consensus:
160 #end if 160 #end if
161 #if $adv_opts.param_precursor_max_charge: 161 #if $adv_opts.param_precursor_max_charge:
162 -precursor:max_charge $adv_opts.param_precursor_max_charge 162 -precursor:max_charge $adv_opts.param_precursor_max_charge
163 #end if 163 #end if
164 #end if 164 #end if
165 </command> 165 ]]></command>
166 <inputs> 166 <inputs>
167 <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing the spectra" help="(-in) "/> 167 <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing the spectra" help="(-in) "/>
168 <param name="param_consensus" type="data" format="consensusxml" optional="False" label="Input file containing the linked mass peaks" help="(-consensus) "/> 168 <param name="param_consensus" type="data" format="consensusxml" optional="False" label="Input file containing the linked mass peaks" help="(-consensus) "/>
169 <param name="param_database" type="data" format="fasta" optional="False" label="Input file containing the protein database" help="(-database) "/> 169 <param name="param_database" type="data" format="fasta" optional="False" label="Input file containing the protein database" help="(-database) "/>
170 <param name="param_decoy_string" type="text" size="30" value="decoy" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) "> 170 <param name="param_decoy_string" type="text" size="30" value="decoy" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">
5338 <data name="param_out_mzIdentML" format="mzid"/> 5338 <data name="param_out_mzIdentML" format="mzid"/>
5339 </outputs> 5339 </outputs>
5340 <help>Tool for protein-protein cross-linking identification using labeled linkers. 5340 <help>Tool for protein-protein cross-linking identification using labeled linkers.
5341 5341
5342 5342
5343 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenPepXL.html</help> 5343 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenPepXL.html</help>
5344 </tool> 5344 </tool>