Mercurial > repos > mmonsoor > probmetab

annotate macros.xml @ 3:f24b9c360a60 draft

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author lecorguille
date Wed, 15 Feb 2017 11:45:26 -0500
parents 9541ba588de1
children a1b528cba999
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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="1.0">r-probmetab</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="stdio">
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11 <stdio>
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12 <exit_code range="1" level="fatal" />
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13 </stdio>
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14 </xml>
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15
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16 <token name="@COMMAND_CAMERA_SCRIPT@">
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17 LANG=C Rscript $__tool_directory__/probmetab.r
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18 </token>
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19
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20 <token name="@COMMAND_LOG_EXIT@">
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21 ;
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22 return=\$?;
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23 mv log.txt '$log';
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24 cat '$log';
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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 <!-- raw file load for planemo test -->
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29 <token name="@COMMAND_FILE_LOAD_NEUTRAL@">
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30 #if $file_load_section_selected.file_load_conditional.file_load_select == "yes":
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31 #if $file_load_section_selected.file_load_conditional.inputs.input == "zip_file":
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32 zipfile$polarity '$file_load_section_selected.file_load_conditional.inputs.zip_file'
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33 #else
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34 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] )
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35 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] )
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36
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37 singlefile_galaxyPath$polarity '$singlefile_galaxyPath'
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38 singlefile_sampleName$polarity '$singlefile_sampleName'
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39 #end if
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40 #end if
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41 </token>
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42
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43 <token name="@COMMAND_FILE_LOAD_ONE@">
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44 #set file_load_section_selected = $file_load_section
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45 #set polarity=""
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46 @COMMAND_FILE_LOAD_NEUTRAL@
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47 </token>
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48
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49 <token name="@COMMAND_FILE_LOAD_POSITIVE@">
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50 #set file_load_section_selected = $file_load_sectionPositive
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51 #set polarity="Positive"
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52 @COMMAND_FILE_LOAD_NEUTRAL@
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53 </token>
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54
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55 <token name="@COMMAND_FILE_LOAD_NEGATIVE@">
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56 #set file_load_section_selected = $file_load_sectionNegative
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57 #set polarity="Negative"
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58 @COMMAND_FILE_LOAD_NEUTRAL@
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59 </token>
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60
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61 <xml name="input_file_load" token_polarity="">
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62 <section name="file_load_section@POLARITY@" title="@POLARITY@ Resubmit your raw dataset or your zip file">
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63 <conditional name="file_load_conditional">
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64 <param name="file_load_select" type="select" label="@POLARITY@ 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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65 <option value="no" >no need</option>
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66 <option value="yes" >yes</option>
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67 </param>
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68 <when value="no">
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69 </when>
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70 <when value="yes">
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71 <conditional name="inputs">
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72 <param name="input" type="select" label="Choose your inputs method" >
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73 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
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74 <option value="single_file">A mzXML or netCDF file from your history</option>
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75 </param>
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76 <when value="zip_file">
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77 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
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78 </when>
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79 <when value="single_file">
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80 <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/>
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81 </when>
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82 </conditional>
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83 </when>
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84 </conditional>
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85 </section>
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86 </xml>
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87
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88 <xml name="test_file_load_zip">
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89 <section name="file_load_section">
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90 <conditional name="file_load_conditional">
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91 <param name="file_load_select" value="yes" />
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92 <conditional name="inputs">
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93 <param name="input" value="zip_file" />
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94 <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" />
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95 </conditional>
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96 </conditional>
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97 </section>
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98 </xml>
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99
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100 <xml name="test_file_load_single" token_polarity="">>
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101 <section name="file_load_section@POLARITY@">
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102 <conditional name="file_load_conditional">
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103 <param name="file_load_select" value="yes" />
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104 <conditional name="inputs">
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105 <param name="input" value="single_file" />
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106 <param name="single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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107 </conditional>
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108 </conditional>
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109 </section>
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110 </xml>
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111
1
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112 <token name="@HELP_AUTHORS@">
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113 .. class:: infomark
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114
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115 **Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br
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116
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117 | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics..
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118 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/
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119
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120 .. class:: infomark
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121
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122 **Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff.
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123
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124 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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125
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126 .. class:: infomark
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127
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128 **Contributors** Ricardo R. Silva rsilvabioinfo@usp.br, Yann Guitton yann.guitton@univ-nantes.fr and Jean-François Martin jean-francois.martin@toulouse.inra.fr
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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">10.1093/bioinformatics/btu019</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>