Mercurial > repos > mmonsoor > probmetab

comparison macros.xml @ 1:c4bd0c40eb3b draft

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planemo upload commit 1c73dd5ed7b5b8595963e0e1b6f8427978d8d5f5-dirty
author lecorguille
date Mon, 04 Jul 2016 09:51:51 -0400
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children 3a9914b37f2f
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0:e13ec2c3fabe 1:c4bd0c40eb3b
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="0.4_1">r-snow</requirement>
6 <requirement type="package" version="1.0">r-probmetab</requirement>
7 <requirement type="package" version="1.1_4">r-batch</requirement>
8 </requirements>
9 </xml>
10 <xml name="stdio">
11 <stdio>
12 <exit_code range="1" level="fatal" />
13 </stdio>
14 </xml>
15
16 <token name="@COMMAND_CAMERA_SCRIPT@">
17 LANG=C Rscript $__tool_directory__/probmetab.r
18 </token>
19
20 <!-- zipfile load for planemo test -->
21 <token name="@COMMAND_ZIPFILE_LOAD@">
22 #if $zipfile_load_conditional.zip_file:
23 zipfile $zipfile_load_conditional.zip_file
24 #end if
25 </token>
26 <xml name="zipfile_load">
27 <conditional name="zipfile_load_conditional">
28 <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
29 <option value="no" >no need</option>
30 <option value="yes" selected="peakgroups">yes</option>
31 </param>
32 <when value="no">
33 </when>
34 <when value="yes">
35 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
36 </when>
37 </conditional>
38 </xml>
39
40 <token name="@HELP_AUTHORS@">
41 .. class:: infomark
42
43 **Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br
44
45 | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics..
46 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/
47
48 .. class:: infomark
49
50 **Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff.
51
52 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
53
54 .. class:: infomark
55
56 **Contributors** Ricardo R. Silva rsilvabioinfo@usp.br, Yann Guitton yann.guitton@univ-nantes.fr and Jean-François Martin jean-francois.martin@toulouse.inra.fr
57
58 ---------------------------------------------------
59
60 </token>
61
62
63 <xml name="citation">
64 <citations>
65 <citation type="doi">10.1093/bioinformatics/btu019</citation>
66 <citation type="doi">10.1093/bioinformatics/btu813</citation>
67 </citations>
68 </xml>
69 </macros>