Mercurial > repos > lecorguille > camera_annotate

annotate macros.xml @ 37:636e36a64d31 draft

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author lecorguille
date Tue, 09 Apr 2019 11:36:39 -0400
parents b02797fbead1
children 2184c0435edf
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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_3">r-snow</requirement>
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6 <requirement type="package" version="1.38.1">bioconductor-camera</requirement>
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7 <requirement type="package" version="2.38.0">bioconductor-multtest</requirement>
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8 <requirement type="package" version="1.1_4">r-batch</requirement>
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9 <requirement type="package" version="1.3.26">graphicsmagick</requirement>
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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_CAMERA_SCRIPT@">
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19 LC_ALL=C Rscript $__tool_directory__/CAMERA.r
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20 </token>
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21
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22 <!-- raw file load for planemo test -->
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23 <token name="@COMMAND_FILE_LOAD@">
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24 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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25 #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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26 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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27 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
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28 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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29 #else
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30 zipfile '$file_load_section.file_load_conditional.input'
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31 #end if
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32 #end if
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33 </token>
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34
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35 <xml name="input_file_load">
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36 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
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37 <conditional name="file_load_conditional">
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38 <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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39 <option value="no" >no need</option>
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40 <option value="yes" >yes</option>
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41 </param>
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42 <when value="no">
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43 </when>
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44 <when value="yes">
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45 <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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46 </when>
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47 </conditional>
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48 </section>
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49 </xml>
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50
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51 <xml name="test_file_load_zip">
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52 <section name="file_load_section">
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53 <conditional name="file_load_conditional">
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54 <param name="file_load_select" value="yes" />
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55 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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56 </conditional>
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57 </section>
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58 </xml>
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59
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60 <xml name="test_file_load_single">
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61 <section name="file_load_section">
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62 <conditional name="file_load_conditional">
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63 <param name="file_load_select" value="yes" />
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64 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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65 </conditional>
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66 </section>
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67 </xml>
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68
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69 <!-- peaklist export option management -->
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70 <token name="@COMMAND_PEAKLIST@">
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71 convertRTMinute $export.convertRTMinute
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72 numDigitsMZ $export.numDigitsMZ
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73 numDigitsRT $export.numDigitsRT
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74 intval $export.intval
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75 </token>
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76
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77 <xml name="input_peaklist">
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78 <section name="export" title="Export options">
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79 <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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80 <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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81 <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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82 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
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83 <option value="into" selected="true">into</option>
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84 <option value="maxo" >maxo</option>
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85 <option value="intb">intb</option>
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86 </param>
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87 </section>
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88 </xml>
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89
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90 <xml name="test_peaklist">
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91 <section name="export">
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92 <param name="convertRTMinute" value="True"/>
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93 <param name="numDigitsMZ" value="4" />
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94 <param name="numDigitsRT" value="1" />
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95 <param name="intval" value="into"/>
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96 </section>
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97 </xml>
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98
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99 <!-- annotate_diffreport <test> commun part -->
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100 <xml name="test_annotate_diffreport">
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101 <section name="groupfwhm">
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102 <param name="sigma" value="6"/>
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103 <param name="perfwhm" value="0.6"/>
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104 </section>
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105 <section name="findisotopes">
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106 <param name="maxcharge" value="3"/>
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107 <param name="maxiso" value="4"/>
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108 <param name="minfrac" value="0.5"/>
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109 </section>
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110 <section name="findgeneral">
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111 <param name="ppm" value="5"/>
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112 <param name="mzabs" value="0.015"/>
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113 <param name="max_peaks" value="100"/>
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114 </section>
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115 <section name="diffreport">
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116 <conditional name="options">
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117 <param name="option" value="show"/>
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118 <param name="eicmax" value="200"/>
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119 <param name="eicwidth" value="200"/>
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120 <param name="value" value="into"/>
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121 <param name="h" value="480"/>
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122 <param name="w" value="640"/>
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123 <param name="mzdec" value="2"/>
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124 <param name="sortpval" value="False"/>
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125 </conditional>
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126 </section>
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127 <expand macro="test_peaklist"/>
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128 </xml>
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129
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130 <xml name="test_annotate_quick_false">
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131 <param name="quick" value="FALSE"/>
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132 <section name="groupcorr">
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133 <param name="cor_eic_th" value="0.75"/>
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134 <param name="graphMethod" value="hcs"/>
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135 <param name="pval" value="0.05"/>
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136 <param name="calcCiS" value="True"/>
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137 <param name="calcIso" value="False"/>
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138 <param name="calcCaS" value="False"/>
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139 </section>
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140 </xml>
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141
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142 <xml name="test_annotate_quick_true">
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143 <conditional name="quick_block">
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144 <param name="quick" value="TRUE"/>
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145 </conditional>
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146 </xml>
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147
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148 <token name="@HELP_AUTHORS@">
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149 .. class:: infomark
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150
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151 **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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152
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153 .. class:: infomark
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154
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155 **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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156
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157 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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158
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159 ---------------------------------------------------
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160
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161 </token>
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162
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163
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164 <xml name="citation">
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165 <citations>
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166 <citation type="doi">10.1021/ac202450g</citation>
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167 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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168 </citations>
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169 </xml>
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170 </macros>