Mercurial > repos > lecorguille > xcms_retcor

annotate macros.xml @ 27:30410a052ab3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
author lecorguille
date Tue, 24 Oct 2017 11:47:49 -0400
parents dcca50c5e1cb
children c013ed353a2f
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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
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16 <xml name="stdio">
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17 <stdio>
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18 <exit_code range="1" level="fatal" />
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19 </stdio>
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20 </xml>
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21
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22 <token name="@COMMAND_XCMS_SCRIPT@">
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23 LANG=C Rscript $__tool_directory__/xcms.r
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24 </token>
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25
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26 <token name="@COMMAND_LOG_EXIT@">
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27 ;
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28 return=\$?;
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29 mv log.txt '$log';
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30 cat '$log';
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31 sh -c "exit \$return"
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32 </token>
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34 <!-- zipfile load for planemo test -->
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36 <token name="@COMMAND_FILE_LOAD@">
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37 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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38 #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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39 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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40 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
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42 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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43 #else
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44 zipfile '$file_load_section.file_load_conditional.input'
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45 #end if
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46 #end if
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47 </token>
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48
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49 <xml name="input_file_load">
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50 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
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51 <conditional name="file_load_conditional">
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52 <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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53 <option value="no" >no need</option>
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54 <option value="yes" >yes</option>
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55 </param>
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56 <when value="no">
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57 </when>
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58 <when value="yes">
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59 <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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60 </when>
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61 </conditional>
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62 </section>
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63 </xml>
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65 <xml name="test_file_load_zip">
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66 <section name="file_load_section">
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67 <conditional name="file_load_conditional">
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68 <param name="file_load_select" value="yes" />
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69 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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70 </conditional>
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71 </section>
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72 </xml>
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73
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74 <xml name="test_file_load_single">
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75 <section name="file_load_section">
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76 <conditional name="file_load_conditional">
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77 <param name="file_load_select" value="yes" />
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78 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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79 </conditional>
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80 </section>
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81 </xml>
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82
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83 <token name="@COMMAND_PEAKLIST@">
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84 #if $peaklist.peaklistBool
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85 variableMetadataOutput '$variableMetadata'
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86 dataMatrixOutput '$dataMatrix'
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87 convertRTMinute $peaklist.convertRTMinute
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88 numDigitsMZ $peaklist.numDigitsMZ
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89 numDigitsRT $peaklist.numDigitsRT
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90 intval $peaklist.intval
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91 #end if
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92 </token>
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94 <xml name="input_peaklist">
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95 <conditional name="peaklist">
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96 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
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97 <when value="true">
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98 <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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99 <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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100 <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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101 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
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102 <option value="into" selected="true">into</option>
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103 <option value="maxo">maxo</option>
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104 <option value="intb">intb</option>
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105 </param>
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106 </when>
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107 <when value="false" />
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108 </conditional>
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109 </xml>
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110
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111 <xml name="output_peaklist" token_function="">
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112 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
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113 <filter>(peaklist['peaklistBool'])</filter>
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114 </data>
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115 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
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116 <filter>(peaklist['peaklistBool'])</filter>
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117 </data>
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118 </xml>
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119
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120 <xml name="input_tic_bpc_pdf">
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121 <param name="tic_bpc_pdf" type="boolean" checked="False" label="Do you want TIC and BCP in PDF Format" help="Whatever, you will be able to use MultiQC tools on the tabular files" />
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122 </xml>
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123
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124 <xml name="test_retcor_param">
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125 <param name="methods|method" value="peakgroups"/>
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126 <param name="methods|smooth" value="loess"/>
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127 <param name="methods|extra" value="1"/>
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128 <param name="methods|missing" value="1"/>
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129 <param name="methods|options|option" value="show"/>
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130 <param name="methods|options|span" value="0.2"/>
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131 <param name="methods|options|family" value="gaussian"/>
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132 <param name="methods|options|plottype" value="deviation"/>
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133 </xml>
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134
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135 <xml name="test_retcor_output" token_raworcorrected="">
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136 <output name="log">
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137 <assert_contents>
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138 <has_text text="object with 4 samples" />
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139 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
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140 <has_text text="Mass range: 200.1-600 m/z" />
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141 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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142 <has_text text="Peak Groups: 0" />
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143 <has_text text="Sample classes: KO, WT" />
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144 </assert_contents>
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145 </output>
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146 <output_collection name="ticsCorrectedTabCollection" type="list">
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147 <element name="ko15" value="ko15-TIC@RAWORCORRECTED@_mqc.out" />
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148 <element name="ko16" value="ko16-TIC@RAWORCORRECTED@_mqc.out" />
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149 <element name="wt15" value="wt15-TIC@RAWORCORRECTED@_mqc.out" />
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150 <element name="wt16" value="wt16-TIC@RAWORCORRECTED@_mqc.out" />
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151 </output_collection>
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152 <output_collection name="bpcsCorrectedTabCollection" type="list">
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153 <element name="ko15" value="ko15-BPC@RAWORCORRECTED@_mqc.out" />
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154 <element name="ko16" value="ko16-BPC@RAWORCORRECTED@_mqc.out" />
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155 <element name="wt15" value="wt15-BPC@RAWORCORRECTED@_mqc.out" />
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156 <element name="wt16" value="wt16-BPC@RAWORCORRECTED@_mqc.out" />
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157 </output_collection>
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158 </xml>
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159
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160 <token name="@HELP_AUTHORS@">
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161
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162 .. class:: infomark
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163
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164 **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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165
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166 .. class:: infomark
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167
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168 **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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169
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170 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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171
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172 ---------------------------------------------------
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173
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174 </token>
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175
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176 <token name="@HELP_BCP_TIC@">
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177
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178 BPCs and TICs: tabular
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179
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180 | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs
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181 | Import BPC and TIC from xcmsSet and retcor [at once] within MultiQC_ (in or outside Galaxy) to display and navigate in the graphs.
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182 | - In MultiQC: as tool, use the Custom Content
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183
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184 .. _MultiQC: http://multiqc.info/
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185
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186 BPCs and TICs: pdf [if using zip]
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187
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188 | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs in pdf format.
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189
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190 </token>
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191
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192 <token name="@HELP_GET_PEAK_LIST@">
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193
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194 Get a Peak List
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195 ---------------
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196
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197 If 'true', the module generates two additional files corresponding to the peak list:
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198 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
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199 - the data matrix (corresponding to related intensities)
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200
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201 **decimal places for [mass or retention time] values in identifiers**
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202
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203 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
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204 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
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205 | Theses parameters do not affect decimal places in columns other than the identifier one.
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206
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207 **Reported intensity values**
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208
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209 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
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210 | - into: integrated area of original (raw) peak
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211 | - maxo: maximum intensity of original (raw) peak
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212 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
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213
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214 </token>
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215
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216 <token name="@HELP_GET_PEAK_LIST_OUTPUTS@">
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217
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218 xset.variableMetadata.tsv : tabular format [If Get a Peak List == Yes]
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219
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220 | Table containing information about ions - Can be used in **Normalisation/Generic_filter** and **Statitics** tools.
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221
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222 xset.dataMatrix.tsv : tabular format
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223
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224 | Table containing ions' intensities - Can be used **Normalisation/Generic_filter** and **Statitics** tools.
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225
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226 </token>
6
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227
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228 <xml name="citation">
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229 <citations>
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230 <citation type="doi">10.1021/ac051437y</citation>
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231 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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232 </citations>
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233 </xml>
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234 </macros>