Mercurial > repos > lecorguille > xcms_fillpeaks

annotate macros.xml @ 11:1bf47b3988fd 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 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
author lecorguille
date Mon, 04 Jul 2016 11:55:28 -0400
parents 35269602a971
children 8a23c743e6ea
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
1 <?xml version="1.0"?>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
2 <macros>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
3 <xml name="requirements">
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
4 <requirements>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
5 <requirement type="package" version="3.1.2">R</requirement>
10
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
6 <requirement type="package" version="0.4_1">r-snow</requirement>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
7 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
8 <requirement type="package" version="1.1_4">r-batch</requirement>
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
9 </requirements>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
10 </xml>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
11 <xml name="stdio">
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
12 <stdio>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
13 <exit_code range="1" level="fatal" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
14 </stdio>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
15 </xml>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
16
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
17 <token name="@COMMAND_XCMS_SCRIPT@">
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
18 LANG=C Rscript $__tool_directory__/xcms.r
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
19 </token>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
20
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
21 <token name="@COMMAND_LOG_EXIT@">
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
22 ;
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
23 return=\$?;
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
24 mv log.txt $log;
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
25 cat $log;
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
26 sh -c "exit \$return"
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
27 </token>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
28
10
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
29 <!-- zipfile load for planemo test -->
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
30
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
31 <token name="@COMMAND_ZIPFILE_LOAD@">
11
1bf47b3988fd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
lecorguille
parents: 10
diff changeset
32 #if $zipfile_load_conditional.zipfile_load_select == "yes":
1bf47b3988fd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
lecorguille
parents: 10
diff changeset
33 #if $zipfile_load_conditional.zip_file:
1bf47b3988fd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
lecorguille
parents: 10
diff changeset
34 zipfile $zipfile_load_conditional.zip_file
1bf47b3988fd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
lecorguille
parents: 10
diff changeset
35 #end if
10
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
36 #end if
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
37 </token>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
38
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
39 <xml name="zipfile_load">
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
40 <conditional name="zipfile_load_conditional">
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
41 <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." >
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
42 <option value="no" >no need</option>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
43 <option value="yes" selected="peakgroups">yes</option>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
44 </param>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
45 <when value="no">
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
46 </when>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
47 <when value="yes">
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
48 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
49 </when>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
50 </conditional>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
51 </xml>
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
52
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
53
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 6
diff changeset
54
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
55 <token name="@HELP_AUTHORS@">
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
56 .. class:: infomark
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
57
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
58 **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
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
59
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
60 .. class:: infomark
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
61
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
62 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
63
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
64 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
65
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
66 ---------------------------------------------------
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
67
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
68 </token>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
69
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
70
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
71 <xml name="citation">
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
72 <citations>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
73 <citation type="doi">10.1021/ac051437y</citation>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
74 <citation type="doi">10.1093/bioinformatics/btu813</citation>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
75 </citations>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
76 </xml>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
77 </macros>