Mercurial > repos > galaxyp > openms_openswathanalyzer

comparison OpenSwathAnalyzer.xml @ 7:9f0a3a6b5df6 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 04:52:46 -0400
parents de254355ce13
children bc57c90ba60f
comparison
equal deleted inserted replaced
6:605bfaea237a 7:9f0a3a6b5df6
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>OpenSwathAnalyzer 13 <command detect_errors="aggressive"><![CDATA[OpenSwathAnalyzer
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_tr: 18 #if $param_tr:
286 #end if 286 #end if
287 #if $adv_opts.param_algorithm_Scores_use_uis_scores: 287 #if $adv_opts.param_algorithm_Scores_use_uis_scores:
288 -algorithm:Scores:use_uis_scores 288 -algorithm:Scores:use_uis_scores
289 #end if 289 #end if
290 #end if 290 #end if
291 </command> 291 ]]></command>
292 <inputs> 292 <inputs>
293 <param name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/> 293 <param name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/>
294 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/> 294 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
295 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/> 295 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/>
296 <param name="param_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/> 296 <param name="param_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/>
418 <data name="param_out" format="featurexml"/> 418 <data name="param_out" format="featurexml"/>
419 </outputs> 419 </outputs>
420 <help>Picks peaks and finds features in an SWATH-MS or SRM experiment. 420 <help>Picks peaks and finds features in an SWATH-MS or SRM experiment.
421 421
422 422
423 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html</help> 423 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathAnalyzer.html</help>
424 </tool> 424 </tool>