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annotate macros.xml @ 17:64fb820146f5 draft

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author lecorguille
date Mon, 04 Jul 2016 11:57:04 -0400
parents af2d29943e97
children 10176a940ec6
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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="3.1.2">R</requirement>
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6 <requirement type="package" version="0.4_1">r-snow</requirement>
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7 <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
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8 <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>
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9 <requirement type="package" version="1.1_4">r-batch</requirement>
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10 <requirement type="package" version="1.6.17">libpng</requirement>
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11 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
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12 </requirements>
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13 </xml>
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14 <xml name="stdio">
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15 <stdio>
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16 <exit_code range="1" level="fatal" />
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17 </stdio>
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18 </xml>
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19
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20 <token name="@COMMAND_CAMERA_SCRIPT@">
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21 LANG=C Rscript $__tool_directory__/CAMERA.r
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22 </token>
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23
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24 <!-- zipfile load for planemo test -->
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25 <token name="@COMMAND_ZIPFILE_LOAD@">
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26 #if $zipfile_load_conditional.zipfile_load_select == "yes":
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27 #if $zipfile_load_conditional.zip_file:
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28 zipfile $zipfile_load_conditional.zip_file
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29 #end if
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30 #end if
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31 </token>
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32 <xml name="zipfile_load">
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33 <conditional name="zipfile_load_conditional">
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34 <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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35 <option value="no" >no need</option>
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36 <option value="yes" selected="peakgroups">yes</option>
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37 </param>
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38 <when value="no">
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39 </when>
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40 <when value="yes">
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41 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
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42 </when>
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43 </conditional>
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44 </xml>
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45
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46 <token name="@HELP_AUTHORS@">
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47 .. class:: infomark
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48
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49 **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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50
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51 .. class:: infomark
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52
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53 **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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54
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55 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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56
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57 ---------------------------------------------------
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58
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59 </token>
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62 <xml name="citation">
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63 <citations>
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64 <citation type="doi">10.1021/ac202450g</citation>
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65 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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66 </citations>
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67 </xml>
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68 </macros>