Mercurial > repos > galaxyp > openms_mapalignerposeclustering

comparison MapAlignerPoseClustering.xml @ 4:e86e83ac0cd3 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 08:10:13 -0400
parents 304c13ce9577
children e237cb433a92
comparison
equal deleted inserted replaced
3:7f1786e1c462 4:e86e83ac0cd3
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><![CDATA[ 13 <command detect_errors="aggressive"><![CDATA[
14
15 #import re
14 16
15 mkdir -p ./results_trafoxml ./results_out && 17 mkdir -p ./results_trafoxml ./results_out &&
16 MapAlignerPoseClustering 18 MapAlignerPoseClustering
17 19
18 -in 20 -in
19 #for $infile in $param_in: 21 #for $infile in $param_in:
20 '$infile' 22 '$infile'
21 #end for 23 #end for
22 24
23 -out 25 -out
24 #for $counter,$infile in enumerate($param_in): 26 #for $infile in $param_in:
25 ./results_out/${infile.element_identifier}.${infile.extension} 27 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
28 './results_out/${escaped_element_identifier}.${infile.extension}'
26 #end for 29 #end for
27 30
28 -trafo_out 31 -trafo_out
29 #for $counter,$infile in enumerate($param_in): 32 #for $infile in $param_in:
30 ./results_trafoxml/${infile.element_identifier}.trafoxml 33 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
34 './results_trafoxml/${escaped_element_identifier}.trafoxml'
31 #end for 35 #end for
32 36
33 #if $param_reference_file: 37 #if $param_reference_file:
34 -reference:file $param_reference_file 38 -reference:file $param_reference_file
35 #end if 39 #end if
182 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/> 186 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/>
183 </collection> 187 </collection>
184 </outputs> 188 </outputs>
185 <help>Corrects retention time distortions between maps using a pose clustering approach. 189 <help>Corrects retention time distortions between maps using a pose clustering approach.
186 190
187 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help> 191 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerPoseClustering.html</help>
188 </tool> 192 </tool>