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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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2:b7d807308ab5 3:d5d7aa6e73ed
1 <tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy1">
2 <description>Parser to get meta information from mzML files and create an ISA-Tab structure</description>
3 <requirements>
4 <requirement type="package">zip</requirement>
5 <requirement type="package" version="1.1.1">mzml2isa</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <command detect_errors="exit_code">
11 <![CDATA[
12
13 #if $input.format == "data_collection"
14 mkdir "temp"
15 &&
16 cd "temp"
17 &&
18 #for $fn in $input.source
19 #if str( $fn ).endswith(".dat")
20 ln -s '$fn' '$fn.name'
21 &&
22 #end if
23 #end for
24 cd ..
25 &&
26 #end if
27
28 #if $metadata
29 ln -s '$metadata' 'metadata.json' &&
30 #end if
31
32 mzml2isa -s $name_of_study -o . -i
33
34 #if $input.format == "zip_file"
35 "zip://$input.source"
36 #else if $input.format == "tar_file"
37 "tar://$input.source"
38 #else if $input.format == "data_collection"
39 "temp"
40 #end if
41
42 #if $metadata
43 -m "metadata.json"
44 #end if
45
46 && zip isa.zip i_* a_* s_* && mv isa.zip "$ISA_zip";
47 ]]>
48 </command>
49 <inputs>
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" />
51 <conditional name="input">
52 <param name="format" type="select" label="Choose the source for the dataset (zip, tar or data collection)" >
53 <option value="zip_file" selected="true">Zip file from your History containing a folder of *.mzML files</option>
54 <option value="tar_file">TAR file from your history containing a folder of *.mzML files</option>
55 <option value="data_collection">Data collection (*.mzML files)</option>
56 </param>
57 <when value="zip_file">
58 <param name="source" type="data" format="zip" label="Zip file from your History containing *.mzml files">
59 </param>
60 </when>
61 <when value="tar_file">
62 <param name="source" type="data" format="tar" label="TAR file from your History containing *.mzml files"/>
63 </when>
64 <when value="data_collection">
65 <param name="source" type="data_collection" format="mzml" label="Data collection of *.mzml" >
66 </param>
67 </when>
68 </conditional>
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"/>
70 </inputs>
71 <outputs>
72 <data name="ISA_zip" format="zip" label="ISA Zip file"/>
73 <collection type="list" label="Assay files" name="a_files">
74 <discover_datasets pattern="(?P&lt;designation&gt;a_.+)\.txt" directory="." format="tabular"/>
75 </collection>
76 <collection type="list" label="Study files" name="s_files">
77 <discover_datasets pattern="(?P&lt;designation&gt;s_.+)\.txt" directory="." format="tabular"/>
78 </collection>
79 <data name="i_file" format="tabular" label="Investigation file" from_work_dir="i_Investigation.txt"/>
80 </outputs>
81 <tests>
82 <test>
83 <param name="name_of_study" value="test" />
84 <param name="input|format" value="zip_file" />
85 <param name="input|source" value="metabolomics_study.zip" ftype="zip" />
86 <output name="i_file" value="i_Investigation.txt" />
87 <output_collection name="a_files" type="list" count="1">
88 <element name="a_test_metabolite_profiling_mass_spectrometry">
89 <assert_contents>
90 <has_n_columns n="80" />
91 </assert_contents>
92 </element>
93 </output_collection>
94 <output_collection name="s_files" type="list" count="1">
95 <element name="s_test">
96 <assert_contents>
97 <has_n_columns n="12" />
98 </assert_contents>
99 </element>
100 </output_collection>
101 </test>
102 <test>
103 <param name="name_of_study" value="test" />
104 <param name="input|format" value="data_collection" />
105 <param name="input|source" >
106 <collection type="list">
107 <element name="1_samp" value="1_samp.mzML" />
108 <element name="2_samp" value="2_samp.mzML" />
109 <element name="3_samp" value="3_samp.mzML" />
110 <element name="4_samp" value="4_samp.mzML" />
111 <element name="5_samp" value="5_samp.mzML" />
112 <element name="6_samp" value="6_samp.mzML" />
113 </collection>
114 </param >
115 <output name="i_file" value="i_Investigation.txt" />
116 <output_collection name="a_files" type="list" count="1">
117 <element name="a_test_metabolite_profiling_mass_spectrometry">
118 <assert_contents>
119 <has_n_columns n="80" />
120 </assert_contents>
121 </element>
122 </output_collection>
123 <output_collection name="s_files" type="list" count="1">
124 <element name="s_test">
125 <assert_contents>
126 <has_n_columns n="12" />
127 </assert_contents>
128 </element>
129 </output_collection>
130 </test>
131 </tests>
132 <help><![CDATA[
133 **Overview**
134 A program to automatically generate ISA-Tab metadata files from metabolomics raw XML (mzML and imzML) data files.
135
136 Additional meta-information not found within the mzML file can be added through a JSON file.
137 However, it is recommended that the mzML2ISA tool is used to create a semi-completed ISA-Tab file structure
138 that is further annotated using ISAcreator https://github.com/ISA-tools/ISAcreator or via the ISA-API.
139
140 .. image::mzml2isa.png
141 ]]></help>
142 <citations>
143 <citation type="doi">10.1002/0471250953.bi1413s53</citation>
144 <citation type="doi">10.1007/s11306-015-0879-3</citation>
145 <citation type="doi">10.1038/ng.1054</citation>
146 </citations>
147 </tool>