Mercurial > repos > workflow4metabolomics > metams_plot

comparison macros.xml @ 0:b60dc620bd14 draft

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planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
author workflow4metabolomics
date Wed, 03 Jul 2019 05:08:14 -0400
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children ba609408eee9
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-1:000000000000 0:b60dc620bd14
1 <?xml version="1.0"?>
2
3 <macros>
4
5 <xml name="stdio">
6 <stdio>
7 <exit_code range="1" level="fatal" />
8 </stdio>
9 </xml>
10
11 <xml name="requirements">
12 <requirements>
13 <requirement type="package" version="1.18.1">bioconductor-metams</requirement>
14 <requirement type="package" version="1.1_4">r-batch</requirement>
15 <yield />
16 </requirements>
17 </xml>
18
19 <xml name="input_file_load">
20 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
21 <conditional name="file_load_conditional">
22 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >
23 <option value="no" >no need</option>
24 <option value="yes" >yes</option>
25 </param>
26 <when value="no">
27 </when>
28 <when value="yes">
29 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
30 </when>
31 </conditional>
32 </section>
33 </xml>
34
35 <!--<xml name="test_file_load_alg">
36 <section name="file_load_section">
37 <conditional name="file_load_conditional">
38 <param name="file_load_select" value="yes" />
39 <param name="input" value="RawFilesTest_alg2_t.mzData,RawFilesTest_alg3_t.mzData,RawFilesTest_alg7_t.mzData,RawFilesTest_alg8_t.mzData,RawFilesTest_alg9_t.mzData,RawFilesTest_alg11_t.mzData" ftype="mzdata" />
40 </conditional>
41 </section>
42 </xml>-->
43
44 <xml name="test_file_load_alg_symlink">
45 <section name="file_load_section">
46 <conditional name="file_load_conditional">
47 <param name="file_load_select" value="yes" />
48 <param name="input" value="alg2.mzData,alg3.mzData,alg7.mzData,alg8.mzData,alg9.mzData,alg11.mzData" ftype="mzdata" />
49 </conditional>
50 </section>
51 </xml>
52
53 <!-- COMMAND -->
54 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
55
56 <token name="@COMMAND_LOG_EXIT@">
57 ;
58 return=\$?;
59 cat 'log.txt';
60 sh -c "exit \$return"
61 </token>
62
63 <!-- FILE_LOAD for planemo test -->
64 <!-- Change | for , because I use it in metaMS tool -->
65 <token name="@COMMAND_FILE_LOAD@">
66 #if $file_load_section.file_load_conditional.file_load_select == "yes":
67 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
68 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
69 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
70
71 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
72 #else
73 zipfile '$file_load_section.file_load_conditional.input'
74 #end if
75 #end if
76 </token>
77
78 </macros>