Mercurial > repos > lecorguille > xcms_fillpeaks

annotate macros.xml @ 30:6b5ed508f81f draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:44:47 -0500
parents f6d3e6be4ea3
children 8fd5b5afa24d
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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="1.46.0">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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20
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21 <token name="@COMMAND_XCMS_SCRIPT@">
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22 LC_ALL=C Rscript $__tool_directory__/xcms.r
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23 </token>
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24
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25 <token name="@COMMAND_LOG_EXIT@">
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26 ;
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27 return=\$?;
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28 mv log.txt '$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_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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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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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="@COMMAND_PEAKLIST@">
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83 #if $peaklist.peaklistBool
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84 variableMetadataOutput '$variableMetadata'
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85 dataMatrixOutput '$dataMatrix'
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86 convertRTMinute $peaklist.convertRTMinute
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87 numDigitsMZ $peaklist.numDigitsMZ
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88 numDigitsRT $peaklist.numDigitsRT
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89 intval $peaklist.intval
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90 #end if
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91 </token>
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92
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93 <xml name="input_peaklist">
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94 <conditional name="peaklist">
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95 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
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96 <when value="true">
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97 <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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98 <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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99 <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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100 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
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101 <option value="into" selected="true">into</option>
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102 <option value="maxo">maxo</option>
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103 <option value="intb">intb</option>
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104 </param>
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105 </when>
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106 <when value="false" />
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107 </conditional>
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108 </xml>
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109
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110 <xml name="output_peaklist" token_function="">
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111 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
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112 <filter>(peaklist['peaklistBool'])</filter>
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113 </data>
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114 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
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115 <filter>(peaklist['peaklistBool'])</filter>
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116 </data>
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117 </xml>
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118
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119 <token name="@HELP_AUTHORS@">
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120 .. class:: infomark
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121
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122 **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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123
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124 .. class:: infomark
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125
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126 **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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127
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128 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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129
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130 ---------------------------------------------------
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131
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132 </token>
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133
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134
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135 <xml name="citation">
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136 <citations>
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137 <citation type="doi">10.1021/ac051437y</citation>
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138 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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139 </citations>
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140 </xml>
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141 </macros>