annotate macros.xml @ 9:94eb263cfab4 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 09:53:54 +0000
parents e3c06320f884
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
1 <?xml version="1.0"?>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
2 <macros>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
3 <xml name="stdio">
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
4 <stdio>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
5 <exit_code range="1" level="fatal" />
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
6 </stdio>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
7 </xml>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
8
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
9 <!-- COMMAND -->
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
10 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
11
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
12 <token name="@COMMAND_LOG_EXIT@">
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
13 ;
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
14 return=\$?;
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
15 cat 'log.txt';
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
16 sh -c "exit \$return"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
17 </token>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
18
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
19 <!-- INPUT_VALIDATORS -->
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
20 <xml name="input_validator_range_integer">
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
21 <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
22 </xml>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
23
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
24 <xml name="input_validator_range_float">
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
25 <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
26 </xml>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
27
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
28 <xml name="input_validator_list_integer">
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
29 <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
30 </xml>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
31
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
32
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
33 <token name="@INPUT_IMAGE_LABEL@">RData file</token>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
34 <token name="@INPUT_IMAGE_HELP@">It contains a xcms3::XCMSnExp object (named xdata)</token>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
35
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
36
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
37 <!-- MISC -->
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
38 <token name="@HELP_AUTHORS_WRAPPERS@">
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
39
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
40 .. class:: infomark
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
41
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
42 **Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
43 Part of Workflow4Metabolomics.org [W4M]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
44
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
45 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
46
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
47 </token>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
48
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
49 <xml name="citation_w4m">
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
50 <citation type="doi">10.1093/bioinformatics/btu813</citation>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
51 </xml>
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
52 </macros>