Mercurial > repos > galaxyp > openms_simplesearchengine

comparison SimpleSearchEngine.xml @ 7:3cec90deb64b 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 08:01:25 -0400
parents 242ba7640825
children e42e8b553f7d
comparison
equal deleted inserted replaced
6:a3b09a079597 7:3cec90deb64b
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>SimpleSearchEngine 13 <command detect_errors="aggressive"><![CDATA[SimpleSearchEngine
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_database: 18 #if $param_database:
108 #end if 108 #end if
109 #if $adv_opts.param_report_top_hits: 109 #if $adv_opts.param_report_top_hits:
110 -report:top_hits $adv_opts.param_report_top_hits 110 -report:top_hits $adv_opts.param_report_top_hits
111 #end if 111 #end if
112 #end if 112 #end if
113 </command> 113 ]]></command>
114 <inputs> 114 <inputs>
115 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> 115 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
116 <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/> 116 <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/>
117 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) "> 117 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
118 <option value="leukocyte elastase">leukocyte elastase</option> 118 <option value="leukocyte elastase">leukocyte elastase</option>
5240 </inputs> 5240 </inputs>
5241 <outputs> 5241 <outputs>
5242 <data name="param_out" format="idxml"/> 5242 <data name="param_out" format="idxml"/>
5243 </outputs> 5243 </outputs>
5244 <help>Annotates MS/MS spectra using SimpleSearchEngine. 5244 <help>Annotates MS/MS spectra using SimpleSearchEngine.
5245 5245 </help>
5246
5247 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SimpleSearchEngine.html</help>
5248 </tool> 5246 </tool>