Mercurial > repos > mmonsoor > probmetab

annotate macros.xml @ 3:abcfa1648b66 draft

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author lecorguille
date Fri, 07 Apr 2017 07:14:12 -0400
parents 3a9914b37f2f
children
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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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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 cat 'log.txt';
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24 sh -c "exit \$return"
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25 </token>
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26
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27 <!-- raw file load for planemo test -->
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28 <token name="@COMMAND_FILE_LOAD_NEUTRAL@">
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29 #if $file_load_section_selected.file_load_conditional.file_load_select == "yes":
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30 #if $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("netcdf"):
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31 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
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32 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
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33 singlefile_galaxyPath$polarity '$singlefile_galaxyPath' singlefile_sampleName$polarity '$singlefile_sampleName'
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34 #else
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35 zipfile$polarity '$file_load_section_selected.file_load_conditional.input'
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36 #end if
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37 #end if
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38 </token>
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39
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40 <token name="@COMMAND_FILE_LOAD_ONE@">
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41 #set file_load_section_selected = $acquisition_options.file_load_section
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42 #set polarity=""
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43 @COMMAND_FILE_LOAD_NEUTRAL@
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44 </token>
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45
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46 <token name="@COMMAND_FILE_LOAD_POSITIVE@">
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47 #set file_load_section_selected = $acquisition_options.file_load_sectionPositive
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48 #set polarity="Positive"
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49 @COMMAND_FILE_LOAD_NEUTRAL@
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50 </token>
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51
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52 <token name="@COMMAND_FILE_LOAD_NEGATIVE@">
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53 #set file_load_section_selected = $acquisition_options.file_load_sectionNegative
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54 #set polarity="Negative"
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55 @COMMAND_FILE_LOAD_NEUTRAL@
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56 </token>
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57
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58 <xml name="input_file_load" token_polarity="">
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59 <section name="file_load_section@POLARITY@" title="@POLARITY@ 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="@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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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_commun">
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75 <section name="getannot">
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76 <param name="allowMiss" value="TRUE" />
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77 <conditional name="option_toexclude">
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78 <param name="option" value="hide" />
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79 </conditional>
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80 </section>
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81 <section name="db">
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82 <param name="kegg_db" value="KEGG" />
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83 <param name="ppm_tol" value="8" />
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84 </section>
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85 <section name="export">
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86 <param name="prob" value="count" />
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87 <param name="html" value="FALSE" />
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88 </section>
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89 <section name="reac2cor">
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90 <param name="opt" value="cor" />
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91 <param name="corprob" value="0.8" />
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92 <param name="pcorprob" value="0.8" />
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93 <param name="corths" value="0.75" />
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94 </section>
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95 </xml>
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96
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97 <xml name="test_file_load_zip">
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98 <section name="file_load_section">
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99 <conditional name="file_load_conditional">
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100 <param name="file_load_select" value="yes" />
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101 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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102 </conditional>
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103 </section>
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104 </xml>
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105
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106 <xml name="test_file_load_single" token_polarity="">>
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107 <section name="file_load_section@POLARITY@">
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108 <conditional name="file_load_conditional">
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109 <param name="file_load_select" value="yes" />
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110 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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111 </conditional>
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112 </section>
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113 </xml>
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114
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115 <token name="@HELP_AUTHORS@">
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116 .. class:: infomark
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118 **Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br
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119
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120 | 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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121 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/
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122
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123 .. class:: infomark
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124
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125 **Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr (and Gildas Le Corguillé) from ABIMS TEAM, Station biologique de Roscoff.
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126
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127 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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128
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129 .. class:: infomark
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130
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131 **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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132
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133 ---------------------------------------------------
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135 </token>
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138 <xml name="citation">
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139 <citations>
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140 <citation type="doi">10.1093/bioinformatics/btu019</citation>
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141 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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142 </citations>
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143 </xml>
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144 </macros>