Mercurial > repos > lecorguille > xcms_retcor

annotate macros.xml @ 33:69b5a006fca1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
author lecorguille
date Thu, 08 Mar 2018 05:54:22 -0500
parents 281786a7b9a2
children 9714270678a7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
1 <?xml version="1.0"?>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
2 <macros>
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
3 <token name="@WRAPPER_VERSION@">3.0.0</token>
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
4 <xml name="requirements">
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
5 <requirements>
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
6 <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
7 <requirement type="package" version="1.1_4">r-batch</requirement>
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
9 <requirement type="package" version="6.0">unzip</requirement>
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
10 <yield />
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
11 </requirements>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
12 </xml>
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
13 <xml name="stdio">
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
14 <stdio>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
15 <exit_code range="1" level="fatal" />
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
16 </stdio>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
17 </xml>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
18
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
19 <token name="@COMMAND_XCMS_SCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
20
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
21 <token name="@COMMAND_LOG_EXIT@">
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
22 ;
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
23 return=\$?;
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
24 cat 'log.txt';
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
25 sh -c "exit \$return"
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
26 </token>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
27
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
28 <xml name="input_validator_range_integer">
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
29 <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
30 </xml>
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
32 <xml name="input_validator_range_float">
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
33 <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator>
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
34 </xml>
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
35
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
36 <xml name="input_validator_list_integer">
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
37 <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
38 </xml>
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
39
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
40 <token name="@INPUT_IMAGE_LABEL@">RData file</token>
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
41 <token name="@INPUT_IMAGE_HELP@">It contain a xcms3::XCMSnExp object (named xdata)</token>
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 31
diff changeset
42
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
43 <!-- zipfile load for planemo test -->
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
44
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
45 <token name="@COMMAND_FILE_LOAD@">
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
46 #if $file_load_section.file_load_conditional.file_load_select == "yes":
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
47 #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"):
31
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
48 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
281786a7b9a2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 30
diff changeset
49 #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
50
21
51b9f9452794 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
lecorguille
parents: 19
diff changeset
51 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
52 #else
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
53 zipfile '$file_load_section.file_load_conditional.input'
11
e6abe754a85b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
lecorguille
parents: 10
diff changeset
54 #end if
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
55 #end if
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
56 </token>
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
57
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
58 <xml name="input_file_load">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
59 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
60 <conditional name="file_load_conditional">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
61 <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." >
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
62 <option value="no" >no need</option>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
63 <option value="yes" >yes</option>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
64 </param>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
65 <when value="no">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
66 </when>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
67 <when value="yes">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
68 <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." />
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
69 </when>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
70 </conditional>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
71 </section>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
72 </xml>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
73
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
74 <xml name="test_file_load_zip">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
75 <section name="file_load_section">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
76 <conditional name="file_load_conditional">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
77 <param name="file_load_select" value="yes" />
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
78 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
79 </conditional>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
80 </section>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
81 </xml>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
82
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
83 <xml name="test_file_load_zip_sacuri">
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
84 <section name="file_load_section">
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
85 <conditional name="file_load_conditional">
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
86 <param name="file_load_select" value="yes" />
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
87 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
88 </conditional>
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
89 </section>
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
90 </xml>
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
91
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
92 <xml name="test_file_load_single">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
93 <section name="file_load_section">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
94 <conditional name="file_load_conditional">
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
95 <param name="file_load_select" value="yes" />
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
96 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
97 </conditional>
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
98 </section>
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
99 </xml>
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
100
19
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
101 <token name="@COMMAND_PEAKLIST@">
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
102 #if $peaklist.peaklistBool
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
103 convertRTMinute $peaklist.convertRTMinute
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
104 numDigitsMZ $peaklist.numDigitsMZ
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
105 numDigitsRT $peaklist.numDigitsRT
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
106 intval $peaklist.intval
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
107 #end if
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
108 </token>
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
109
19
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
110 <xml name="input_peaklist">
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
111 <conditional name="peaklist">
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
112 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
113 <when value="true">
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
114 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
115 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
116 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
117 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
118 <option value="into" selected="true">into</option>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
119 <option value="maxo">maxo</option>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
120 <option value="intb">intb</option>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
121 </param>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
122 </when>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
123 <when value="false" />
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
124 </conditional>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
125 </xml>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
126
26
dcca50c5e1cb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 392e432529877680e80a7b338e20d69a42e53767
lecorguille
parents: 22
diff changeset
127 <xml name="output_peaklist" token_function="">
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
128 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
19
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
129 <filter>(peaklist['peaklistBool'])</filter>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
130 </data>
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
131 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
19
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
132 <filter>(peaklist['peaklistBool'])</filter>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
133 </data>
2faecb1270fe planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 18
diff changeset
134 </xml>
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
135
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
136 <token name="@HELP_AUTHORS@">
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
137 .. class:: infomark
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
138
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
139 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
140
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
141 .. class:: infomark
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
142
29
c013ed353a2f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 27
diff changeset
143 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
144
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
145 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
146
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
147 ---------------------------------------------------
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
148
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
149 </token>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
150
30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
151 <token name="@HELP_XCMS_MANUAL@">
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
152
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
153 For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
154
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
155 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
156 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
157 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
158
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
159 </token>
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
160
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
161 <token name="@HELP_PEAKLIST@">
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
162
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
163 Get a Peak List
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
164 ---------------
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
165
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
166 If 'true', the module generates two additional files corresponding to the peak list:
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
167 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
168 - the data matrix (corresponding to related intensities)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
169
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
170 **decimal places for [mass or retention time] values in identifiers**
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
171
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
172 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
173 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
174 | Theses parameters do not affect decimal places in columns other than the identifier one.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
175
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
176 **Reported intensity values**
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
177
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
178 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
179 | - into: integrated area of original (raw) peak
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
180 | - maxo: maximum intensity of original (raw) peak
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
181 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
182
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
183 </token>
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
184
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
185 <xml name="citation">
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
186 <citations>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
187 <citation type="doi">10.1021/ac051437y</citation>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
188 <citation type="doi">10.1093/bioinformatics/btu813</citation>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
189 </citations>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
190 </xml>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
191 </macros>