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annotate macros.xml @ 15:e43f928bbcd2 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
author lecorguille
date Thu, 22 Dec 2016 06:00:29 -0500
parents cb09def13e0d
children 339738598d55
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dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
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1 <?xml version="1.0"?>
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="0.4_1">r-snow</requirement>
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6 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
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7 <requirement type="package" version="1.1_4">r-batch</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="stdio">
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11 <stdio>
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12 <exit_code range="1" level="fatal" />
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13 </stdio>
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14 </xml>
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16 <token name="@COMMAND_XCMS_SCRIPT@">
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17 LANG=C Rscript $__tool_directory__/xcms.r
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18 </token>
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20 <token name="@COMMAND_LOG_EXIT@">
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21 ;
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22 return=\$?;
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23 mv log.txt $log;
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24 cat $log;
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25 sh -c "exit \$return"
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26 </token>
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27
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28 <!-- zipfile load for planemo test -->
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30 <token name="@COMMAND_ZIPFILE_LOAD@">
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31 #if $zipfile_load_conditional.zipfile_load_select == "yes":
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32 #if $zipfile_load_conditional.zip_file:
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33 zipfile $zipfile_load_conditional.zip_file
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34 #end if
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35 #end if
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36 </token>
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38 <xml name="zipfile_load">
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39 <conditional name="zipfile_load_conditional">
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40 <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." >
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41 <option value="no" >no need</option>
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42 <option value="yes" selected="peakgroups">yes</option>
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43 </param>
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44 <when value="no">
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45 </when>
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46 <when value="yes">
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47 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
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48 </when>
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49 </conditional>
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50 </xml>
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53
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54 <token name="@HELP_AUTHORS@">
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55 .. class:: infomark
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57 **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
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59 .. class:: infomark
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61 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
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63 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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65 ---------------------------------------------------
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67 </token>
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70 <xml name="citation">
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71 <citations>
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72 <citation type="doi">10.1021/ac051437y</citation>
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73 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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74 </citations>
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75 </xml>
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76 </macros>