Mercurial > repos > galaxyp > openms_mapalignerposeclustering
comparison MapAlignerPoseClustering.xml @ 4:e86e83ac0cd3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
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date | Wed, 15 May 2019 08:10:13 -0400 |
parents | 304c13ce9577 |
children | e237cb433a92 |
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3:7f1786e1c462 | 4:e86e83ac0cd3 |
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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> |