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annotate macros.xml @ 18:d9e7403f16f3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b3ba169290fd2e40dafe167f345106c1c3da3ebe
author lecorguille
date Wed, 08 Feb 2017 04:37:18 -0500
parents a2908411620e
children 4992ecc91c96
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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="requirements_light">
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11 <requirements>
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12 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
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13 </requirements>
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14 </xml>
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15 <xml name="stdio">
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16 <stdio>
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17 <exit_code range="1" level="fatal" />
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18 </stdio>
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19 </xml>
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21 <token name="@COMMAND_XCMS_SCRIPT@">
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22 LANG=C Rscript $__tool_directory__/xcms.r
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23 </token>
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25 <token name="@COMMAND_LOG_EXIT@">
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26 ;
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27 return=\$?;
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28 mv log.txt $log;
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29 cat $log;
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30 sh -c "exit \$return"
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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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35 <token name="@COMMAND_FILE_LOAD@">
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36 #if $file_load_conditional.file_load_select == "yes":
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37 #if $file_load_conditional.inputs.input == "zip_file":
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38 zipfile $file_load_conditional.inputs.zip_file
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39 #else
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40 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
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41 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )
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43 singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
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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="file_load">
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49 <conditional name="file_load_conditional">
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50 <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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51 <option value="no" >no need</option>
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52 <option value="yes" >yes</option>
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53 </param>
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54 <when value="no">
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55 </when>
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56 <when value="yes">
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57 <conditional name="inputs">
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58 <param name="input" type="select" label="Choose your inputs method" >
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59 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
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60 <option value="single_file">A mzXML or netCDF file from your history</option>
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61 </param>
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62 <when value="zip_file">
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63 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
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64 </when>
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65 <when value="single_file">
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66 <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/>
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67 </when>
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68 </conditional>
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69 </when>
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70 </conditional>
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71 </xml>
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72
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73 <token name="@COMMAND_PEAKLIST@">
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74 #if $peaklist.peaklistBool
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75 variableMetadataOutput $variableMetadata
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76 dataMatrixOutput $dataMatrix
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77 convertRTMinute $peaklist.convertRTMinute
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78 numDigitsMZ $peaklist.numDigitsMZ
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79 numDigitsRT $peaklist.numDigitsRT
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80 intval $peaklist.intval
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81 #end if
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82 </token>
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83
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84 <xml name="input_peaklist">
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85 <conditional name="peaklist">
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86 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
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87 <when value="true">
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88 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
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89 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
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90 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
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91 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
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92 <option value="into" selected="true">into</option>
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93 <option value="maxo">maxo</option>
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94 <option value="intb">intb</option>
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95 </param>
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96 </when>
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97 <when value="false" />
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98 </conditional>
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99 </xml>
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100
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101 <xml name="output_peaklist">
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102 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">
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103 <filter>(peaklist['peaklistBool'])</filter>
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104 </data>
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105 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" >
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106 <filter>(peaklist['peaklistBool'])</filter>
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107 </data>
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108 </xml>
12
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109
9
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110 <token name="@HELP_AUTHORS@">
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111 .. class:: infomark
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112
17
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113 **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
9
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114
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115 .. class:: infomark
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116
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117 **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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118
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119 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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120
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121 ---------------------------------------------------
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122
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123 </token>
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124
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125
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126 <xml name="citation">
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127 <citations>
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128 <citation type="doi">10.1021/ac051437y</citation>
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129 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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130 </citations>
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131 </xml>
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132 </macros>