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annotate macros.xml @ 7:dd0a593dded1 draft

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author lecorguille
date Wed, 12 Apr 2017 08:53:04 -0400
parents 03fdfbd914ab
children 80de755766a8
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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="1.7.5">r-ipo</requirement>
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7 <requirement type="package" version="1.1_4">r-batch</requirement>
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8 <!--<requirement type="package" version="1.7.5">r-ipo-meta</requirement>-->
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9 </requirements>
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10 </xml>
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11 <xml name="stdio">
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12 <stdio>
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13 <exit_code range="1" level="fatal" />
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14 </stdio>
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15 </xml>
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16
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17 <token name="@COMMAND_SCRIPT@">
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18 LANG=C Rscript $__tool_directory__/
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19 </token>
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20
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21 <token name="@COMMAND_LOG_EXIT@">
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22 ;
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23 return=\$?;
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24 mv log.txt $log;
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25 cat $log;
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26 sh -c "exit \$return"
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27 </token>
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28
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29 <token name="@COMMAND_NSLAVES@">
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30 nSlaves \${GALAXY_SLOTS:-1}
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31 </token>
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32
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33 <!-- zipfile load for planemo test -->
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34
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35 <token name="@COMMAND_FILE_LOAD@">
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36 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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37 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
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38 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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39 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
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41 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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42 #else
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43 zipfile '$file_load_section.file_load_conditional.input'
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44 #end if
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45 #end if
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46 </token>
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47
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48 <xml name="input_file_load">
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49 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
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50 <conditional name="file_load_conditional">
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51 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
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52 <option value="no" >no need</option>
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53 <option value="yes" >yes</option>
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54 </param>
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55 <when value="no">
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56 </when>
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57 <when value="yes">
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58 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
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59 </when>
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60 </conditional>
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61 </section>
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62 </xml>
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63
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64 <xml name="test_file_load_zip">
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65 <section name="file_load_section">
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66 <conditional name="file_load_conditional">
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67 <param name="file_load_select" value="yes" />
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68 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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69 </conditional>
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70 </section>
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71 </xml>
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72
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73 <xml name="test_file_load_single">
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74 <section name="file_load_section">
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75 <conditional name="file_load_conditional">
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76 <param name="file_load_select" value="yes" />
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77 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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78 </conditional>
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79 </section>
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80 </xml>
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81
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82 <token name="@HELP_AUTHORS@">
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83 .. class:: infomark
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84
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85 **Authors** Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes
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86
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87 .. class:: infomark
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88
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89 **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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90
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91 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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92
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93 ---------------------------------------------------
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94
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95 </token>
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96
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97
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98 <xml name="citation">
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99 <citations>
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100 <citation type="doi">10.1186/s12859-015-0562-8</citation>
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101 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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102 </citations>
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103 </xml>
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104 </macros>