Mercurial > repos > tomnl > mzml2isa

annotate mzml2isa.xml @ 3:d5d7aa6e73ed draft default tip

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planemo upload for repository https://github.com/ISA-tools/mzml2isa commit 16f55e636c7d9c2be748cb8212184164e57e4b95
author tomnl
date Wed, 07 Dec 2022 17:31:23 +0000
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3
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1 <tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy1">
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2 <description>Parser to get meta information from mzML files and create an ISA-Tab structure</description>
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3 <requirements>
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4 <requirement type="package">zip</requirement>
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5 <requirement type="package" version="1.1.1">mzml2isa</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12
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13 #if $input.format == "data_collection"
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14 mkdir "temp"
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15 &&
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16 cd "temp"
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17 &&
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18 #for $fn in $input.source
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19 #if str( $fn ).endswith(".dat")
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20 ln -s '$fn' '$fn.name'
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21 &&
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22 #end if
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23 #end for
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24 cd ..
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25 &&
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26 #end if
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27
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28 #if $metadata
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29 ln -s '$metadata' 'metadata.json' &&
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30 #end if
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31
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32 mzml2isa -s $name_of_study -o . -i
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33
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34 #if $input.format == "zip_file"
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35 "zip://$input.source"
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36 #else if $input.format == "tar_file"
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37 "tar://$input.source"
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38 #else if $input.format == "data_collection"
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39 "temp"
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40 #end if
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41
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42 #if $metadata
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43 -m "metadata.json"
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44 #end if
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45
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46 && zip isa.zip i_* a_* s_* && mv isa.zip "$ISA_zip";
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47 ]]>
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48 </command>
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49 <inputs>
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50 <param name="name_of_study" type="text" label="Name study" help="This should not contain any spaces as the name will be used a prefix for ISA-tab file names" />
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51 <conditional name="input">
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52 <param name="format" type="select" label="Choose the source for the dataset (zip, tar or data collection)" >
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53 <option value="zip_file" selected="true">Zip file from your History containing a folder of *.mzML files</option>
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54 <option value="tar_file">TAR file from your history containing a folder of *.mzML files</option>
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55 <option value="data_collection">Data collection (*.mzML files)</option>
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56 </param>
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57 <when value="zip_file">
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58 <param name="source" type="data" format="zip" label="Zip file from your History containing *.mzml files">
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59 </param>
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60 </when>
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61 <when value="tar_file">
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62 <param name="source" type="data" format="tar" label="TAR file from your History containing *.mzml files"/>
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63 </when>
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64 <when value="data_collection">
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65 <param name="source" type="data_collection" format="mzml" label="Data collection of *.mzml" >
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66 </param>
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67 </when>
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68 </conditional>
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69 <param optional="true" format="json" name="metadata" type="data" label="Additional user Metadata in json" help="A user can add additional metadata directory through a json file"/>
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70 </inputs>
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71 <outputs>
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72 <data name="ISA_zip" format="zip" label="ISA Zip file"/>
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73 <collection type="list" label="Assay files" name="a_files">
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74 <discover_datasets pattern="(?P&lt;designation&gt;a_.+)\.txt" directory="." format="tabular"/>
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75 </collection>
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76 <collection type="list" label="Study files" name="s_files">
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77 <discover_datasets pattern="(?P&lt;designation&gt;s_.+)\.txt" directory="." format="tabular"/>
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78 </collection>
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79 <data name="i_file" format="tabular" label="Investigation file" from_work_dir="i_Investigation.txt"/>
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="name_of_study" value="test" />
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84 <param name="input|format" value="zip_file" />
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85 <param name="input|source" value="metabolomics_study.zip" ftype="zip" />
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86 <output name="i_file" value="i_Investigation.txt" />
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87 <output_collection name="a_files" type="list" count="1">
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88 <element name="a_test_metabolite_profiling_mass_spectrometry">
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89 <assert_contents>
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90 <has_n_columns n="80" />
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91 </assert_contents>
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92 </element>
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93 </output_collection>
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94 <output_collection name="s_files" type="list" count="1">
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95 <element name="s_test">
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96 <assert_contents>
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97 <has_n_columns n="12" />
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98 </assert_contents>
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99 </element>
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100 </output_collection>
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101 </test>
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102 <test>
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103 <param name="name_of_study" value="test" />
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104 <param name="input|format" value="data_collection" />
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105 <param name="input|source" >
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106 <collection type="list">
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107 <element name="1_samp" value="1_samp.mzML" />
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108 <element name="2_samp" value="2_samp.mzML" />
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109 <element name="3_samp" value="3_samp.mzML" />
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110 <element name="4_samp" value="4_samp.mzML" />
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111 <element name="5_samp" value="5_samp.mzML" />
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112 <element name="6_samp" value="6_samp.mzML" />
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113 </collection>
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114 </param >
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115 <output name="i_file" value="i_Investigation.txt" />
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116 <output_collection name="a_files" type="list" count="1">
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117 <element name="a_test_metabolite_profiling_mass_spectrometry">
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118 <assert_contents>
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119 <has_n_columns n="80" />
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120 </assert_contents>
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121 </element>
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122 </output_collection>
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123 <output_collection name="s_files" type="list" count="1">
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124 <element name="s_test">
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125 <assert_contents>
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126 <has_n_columns n="12" />
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127 </assert_contents>
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128 </element>
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129 </output_collection>
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130 </test>
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131 </tests>
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132 <help><![CDATA[
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133 **Overview**
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134 A program to automatically generate ISA-Tab metadata files from metabolomics raw XML (mzML and imzML) data files.
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135
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136 Additional meta-information not found within the mzML file can be added through a JSON file.
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137 However, it is recommended that the mzML2ISA tool is used to create a semi-completed ISA-Tab file structure
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138 that is further annotated using ISAcreator https://github.com/ISA-tools/ISAcreator or via the ISA-API.
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139
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140 .. image::mzml2isa.png
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141 ]]></help>
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142 <citations>
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143 <citation type="doi">10.1002/0471250953.bi1413s53</citation>
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144 <citation type="doi">10.1007/s11306-015-0879-3</citation>
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145 <citation type="doi">10.1038/ng.1054</citation>
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146 </citations>
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147 </tool>