Mercurial > repos > lecorguille > xcms_fillpeaks

annotate macros.xml @ 31:8fd5b5afa24d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:17:29 -0500
parents 6b5ed508f81f
children 565693681374
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@WRAPPER_VERSION@">3.0.0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</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="1.1_2">r-rcolorbrewer</requirement>
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9 <yield />
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10 </requirements>
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11 </xml>
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12 <xml name="stdio">
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13 <stdio>
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14 <exit_code range="1" level="fatal" />
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15 </stdio>
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16 </xml>
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17
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18 <token name="@COMMAND_XCMS_SCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
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20 <token name="@COMMAND_LOG_EXIT@">
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21 ;
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22 return=\$?;
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23 cat 'log.txt';
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24 sh -c "exit \$return"
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25 </token>
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27 <!-- zipfile load for planemo test -->
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29 <token name="@COMMAND_FILE_LOAD@">
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30 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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31 #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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32 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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33 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
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35 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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36 #else
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37 zipfile '$file_load_section.file_load_conditional.input'
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38 #end if
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39 #end if
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40 </token>
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41
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42 <xml name="input_file_load">
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43 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
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44 <conditional name="file_load_conditional">
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45 <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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46 <option value="no" >no need</option>
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47 <option value="yes" >yes</option>
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48 </param>
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49 <when value="no">
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50 </when>
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51 <when value="yes">
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52 <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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53 </when>
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54 </conditional>
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55 </section>
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56 </xml>
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58 <xml name="test_file_load_zip">
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59 <section name="file_load_section">
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60 <conditional name="file_load_conditional">
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61 <param name="file_load_select" value="yes" />
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62 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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63 </conditional>
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64 </section>
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65 </xml>
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66
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67 <xml name="test_file_load_zip_sacuri">
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68 <section name="file_load_section">
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69 <conditional name="file_load_conditional">
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70 <param name="file_load_select" value="yes" />
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71 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
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72 </conditional>
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73 </section>
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74 </xml>
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75
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76 <xml name="test_file_load_single">
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77 <section name="file_load_section">
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78 <conditional name="file_load_conditional">
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79 <param name="file_load_select" value="yes" />
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80 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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81 </conditional>
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82 </section>
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83 </xml>
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84
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85 <token name="@COMMAND_PEAKLIST@">
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86 #if $peaklist.peaklistBool
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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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93
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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" from_work_dir="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" from_work_dir="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 <token name="@HELP_AUTHORS@">
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121 .. class:: infomark
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122
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123 **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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124
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125 .. class:: infomark
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126
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127 **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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128
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129 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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130
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131 ---------------------------------------------------
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132
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133 </token>
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134
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135 <token name="@HELP_XCMS_MANUAL@">
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136
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137 For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_
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138
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139 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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140 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
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141 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
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142
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143 </token>
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144
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145 <token name="@HELP_PEAKLIST@">
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146
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147 Get a Peak List
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148 ---------------
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149
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150 If 'true', the module generates two additional files corresponding to the peak list:
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151 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
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152 - the data matrix (corresponding to related intensities)
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153
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154 **decimal places for [mass or retention time] values in identifiers**
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155
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156 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
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157 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
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158 | Theses parameters do not affect decimal places in columns other than the identifier one.
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159
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160 **Reported intensity values**
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161
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162 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
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163 | - into: integrated area of original (raw) peak
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164 | - maxo: maximum intensity of original (raw) peak
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165 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
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166
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167 </token>
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168
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169 <xml name="citation">
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170 <citations>
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171 <citation type="doi">10.1021/ac051437y</citation>
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172 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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173 </citations>
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174 </xml>
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175 </macros>