Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate macros.xml @ 0:fe1f0f16d9e6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
author lecorguille
date Thu, 08 Mar 2018 02:48:44 -0500
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children e6fdadaf039e
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fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
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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 <requirement type="package" version="6.0">unzip</requirement>
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10 <yield />
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11 </requirements>
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12 </xml>
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13 <xml name="stdio">
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14 <stdio>
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15 <exit_code range="1" level="fatal" />
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16 </stdio>
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17 </xml>
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18
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19 <token name="@COMMAND_XCMS_SCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
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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 cat 'log.txt';
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25 sh -c "exit \$return"
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26 </token>
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27
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28 <xml name="input_validator_range_integer">
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29 <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
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30 </xml>
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31
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32 <xml name="input_validator_range_float">
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33 <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator>
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34 </xml>
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35
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36 <xml name="input_validator_list_integer">
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37 <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
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38 </xml>
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39
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40 <token name="@INPUT_IMAGE_LABEL@">RData file</token>
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41 <token name="@INPUT_IMAGE_HELP@">It contain a xcms3::XCMSnExp object (named xdata)</token>
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42
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43 <!-- zipfile load for planemo test -->
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44
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45 <token name="@COMMAND_FILE_LOAD@">
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46 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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47 #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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48 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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49 #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
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50
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51 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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52 #else
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53 zipfile '$file_load_section.file_load_conditional.input'
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54 #end if
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55 #end if
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56 </token>
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57
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58 <xml name="input_file_load">
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59 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
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60 <conditional name="file_load_conditional">
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61 <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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62 <option value="no" >no need</option>
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63 <option value="yes" >yes</option>
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64 </param>
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65 <when value="no">
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66 </when>
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67 <when value="yes">
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68 <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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69 </when>
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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_zip">
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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="faahKO_reduce.zip" ftype="zip" />
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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 <xml name="test_file_load_zip_sacuri">
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84 <section name="file_load_section">
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85 <conditional name="file_load_conditional">
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86 <param name="file_load_select" value="yes" />
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87 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
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88 </conditional>
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89 </section>
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90 </xml>
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91
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92 <xml name="test_file_load_single">
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93 <section name="file_load_section">
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94 <conditional name="file_load_conditional">
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95 <param name="file_load_select" value="yes" />
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96 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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97 </conditional>
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98 </section>
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99 </xml>
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100
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101 <token name="@COMMAND_PEAKLIST@">
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102 #if $peaklist.peaklistBool
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103 convertRTMinute $peaklist.convertRTMinute
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104 numDigitsMZ $peaklist.numDigitsMZ
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105 numDigitsRT $peaklist.numDigitsRT
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106 intval $peaklist.intval
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107 #end if
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108 </token>
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109
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110 <xml name="input_peaklist">
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111 <conditional name="peaklist">
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112 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
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113 <when value="true">
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114 <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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115 <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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116 <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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117 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
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118 <option value="into" selected="true">into</option>
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119 <option value="maxo">maxo</option>
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120 <option value="intb">intb</option>
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121 </param>
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122 </when>
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123 <when value="false" />
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124 </conditional>
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125 </xml>
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126
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127 <xml name="output_peaklist" token_function="">
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128 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
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129 <filter>(peaklist['peaklistBool'])</filter>
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130 </data>
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131 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
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132 <filter>(peaklist['peaklistBool'])</filter>
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133 </data>
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134 </xml>
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135
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136 <token name="@HELP_AUTHORS@">
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137 .. class:: infomark
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138
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139 **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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140
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141 .. class:: infomark
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142
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143 **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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144
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145 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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146
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147 ---------------------------------------------------
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148
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149 </token>
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150
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151 <token name="@HELP_XCMS_MANUAL@">
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152
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153 For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_
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154
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155 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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156 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
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157 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
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158
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159 </token>
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160
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161 <token name="@HELP_PEAKLIST@">
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162
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163 Get a Peak List
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164 ---------------
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165
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166 If 'true', the module generates two additional files corresponding to the peak list:
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167 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
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168 - the data matrix (corresponding to related intensities)
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169
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170 **decimal places for [mass or retention time] values in identifiers**
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171
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172 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
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173 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
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174 | Theses parameters do not affect decimal places in columns other than the identifier one.
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175
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176 **Reported intensity values**
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177
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178 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
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179 | - into: integrated area of original (raw) peak
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180 | - maxo: maximum intensity of original (raw) peak
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181 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
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182
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183 </token>
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184
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185 <xml name="citation">
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186 <citations>
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187 <citation type="doi">10.1021/ac051437y</citation>
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188 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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189 </citations>
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190 </xml>
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191 </macros>