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annotate macros.xml @ 1:c4bd0c40eb3b draft

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author lecorguille
date Mon, 04 Jul 2016 09:51:51 -0400
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1 <?xml version="1.0"?>
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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="1.0">r-probmetab</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_CAMERA_SCRIPT@">
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17 LANG=C Rscript $__tool_directory__/probmetab.r
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18 </token>
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20 <!-- zipfile load for planemo test -->
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21 <token name="@COMMAND_ZIPFILE_LOAD@">
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22 #if $zipfile_load_conditional.zip_file:
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23 zipfile $zipfile_load_conditional.zip_file
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24 #end if
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25 </token>
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26 <xml name="zipfile_load">
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27 <conditional name="zipfile_load_conditional">
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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." >
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29 <option value="no" >no need</option>
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30 <option value="yes" selected="peakgroups">yes</option>
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31 </param>
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32 <when value="no">
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33 </when>
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34 <when value="yes">
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35 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
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36 </when>
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37 </conditional>
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38 </xml>
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39
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40 <token name="@HELP_AUTHORS@">
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41 .. class:: infomark
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42
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43 **Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br
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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..
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46 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/
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48 .. class:: infomark
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50 **Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff.
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52 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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54 .. class:: infomark
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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
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58 ---------------------------------------------------
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60 </token>
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63 <xml name="citation">
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64 <citations>
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65 <citation type="doi">10.1093/bioinformatics/btu019</citation>
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66 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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67 </citations>
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68 </xml>
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69 </macros>