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comparison macros.xml @ 6:03fdfbd914ab draft

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planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
author lecorguille
date Thu, 30 Mar 2017 11:27:09 -0400
parents 9fa5856f6184
children dd0a593dded1
comparison
equal deleted inserted replaced
5:d63c80d54b24 6:03fdfbd914ab
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.4_1">r-snow</requirement> 5 <requirement type="package" version="0.4_1">r-snow</requirement>
6 <requirement type="package" version="1.7.5">r-ipo</requirement> 6 <requirement type="package" version="1.7.5">r-ipo</requirement>
7 <requirement type="package" version="1.1_4">r-batch</requirement> 7 <requirement type="package" version="1.1_4">r-batch</requirement>
8 <!--<requirement type="package" version="1.7.5">r-ipo-meta</requirement>-->
8 </requirements> 9 </requirements>
9 </xml> 10 </xml>
10 <xml name="stdio"> 11 <xml name="stdio">
11 <stdio> 12 <stdio>
12 <exit_code range="1" level="fatal" /> 13 <exit_code range="1" level="fatal" />
13 </stdio> 14 </stdio>
14 </xml> 15 </xml>
15 16
16 <token name="@COMMAND_SCRIPT@"> 17 <token name="@COMMAND_SCRIPT@">
17 LANG=C Rscript $__tool_directory__/ipo.r 18 LANG=C Rscript $__tool_directory__/
18 </token> 19 </token>
19 20
20 <token name="@COMMAND_LOG_EXIT@"> 21 <token name="@COMMAND_LOG_EXIT@">
21 ; 22 ;
22 return=\$?; 23 return=\$?;
23 mv log.txt $log; 24 mv log.txt $log;
24 cat $log; 25 cat $log;
25 sh -c "exit \$return" 26 sh -c "exit \$return"
26 </token> 27 </token>
27 28
29 <token name="@COMMAND_NSLAVES@">
30 nSlaves \${GALAXY_SLOTS:-1}
31 </token>
32
33 <!-- zipfile load for planemo test -->
34
35 <token name="@COMMAND_FILE_LOAD@">
36 #if $file_load_conditional.file_load_select == "yes":
37 #if $file_load_conditional.inputs.input == "zip_file":
38 zipfile $file_load_conditional.inputs.zip_file
39 #else
40 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
41 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )
42
43 singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
44 #end if
45 #end if
46 </token>
47
48 <xml name="file_load">
49 <conditional name="file_load_conditional">
50 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
51 <option value="no" >no need</option>
52 <option value="yes" >yes</option>
53 </param>
54 <when value="no">
55 </when>
56 <when value="yes">
57 <conditional name="inputs">
58 <param name="input" type="select" label="Choose your inputs method" >
59 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
60 <option value="single_file">A mzXML or netCDF file from your history</option>
61 </param>
62 <when value="zip_file">
63 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
64 </when>
65 <when value="single_file">
66 <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/>
67 </when>
68 </conditional>
69 </when>
70 </conditional>
71 </xml>
72
28 <token name="@HELP_AUTHORS@"> 73 <token name="@HELP_AUTHORS@">
29 .. class:: infomark 74 .. class:: infomark
30 75
31 **Authors** Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes 76 **Authors** Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes
32 77
33 .. class:: infomark 78 .. class:: infomark
34 79
35 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] 80 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
36 81