Mercurial > repos > galaxyp > pyteomics_mztab2tsv

comparison mztab2tsv.xml @ 0:84e4b5d4b7ad draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
author galaxyp
date Fri, 15 Jan 2021 15:58:54 +0000
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children a475c1906e0b
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-1:000000000000 0:84e4b5d4b7ad
1 <tool id="mztab2tsv" name="pyteomics" version="@TOOL_VERSION@" profile="20.01" license="MIT">
2 <description>convert mztab to tabular</description>
3 <macros>
4 <token name="@TOOL_VERSION@">4.4.1</token>
5 <xml name="output" token_type="" token_label="">
6 <data name="out_@TYPE@" format="tabular" from_work_dir="@TYPE@.tsv" label="${tool.name} on ${on_string}: @LABEL@">
7 <filter>"@TYPE@" in out_select</filter>
8 </data>
9 </xml>
10 </macros>
11 <xrefs>
12 <xref type="bio.tools">pyteomics</xref>
13 </xrefs>
14 <edam_topics>
15 <edam_topic>topic_0121</edam_topic><!-- proteomics -->
16 <edam_topic>topic_3520</edam_topic><!-- proteomics experiment-->
17 </edam_topics>
18 <edam_operations>
19 <edam_operation>operation_3434</edam_operation><!-- Convert a data set from one form to another -->
20 </edam_operations>
21 <requirements>
22 <requirement type="package" version="@TOOL_VERSION@">pyteomics</requirement>
23 </requirements>
24 <command detect_errors="exit_code"><![CDATA[
25 ## make sure that selected outputs exist even if the tool does not generate them
26 #for o in $out_select
27 touch '$o'.tsv &&
28 #end for
29 '$__tool_directory__/mztab_reader.py' --path_in '$path_in'
30 ]]></command>
31 <inputs>
32 <param argument="--path_in" type="data" format="mztab,mztab2" label="mztab or mztab2 data set" help="" />
33 <param name="out_select" type="select" label="Select desired tables" multiple="true" help="">
34 <option value="mtd" selected="true">Metadata (v1,v2)</option>
35 <option value="prt">Protein table (v1)</option>
36 <option value="pep">Peptide table (v1)</option>
37 <option value="psm">Peptide spectrum match table (v1)</option>
38 <option value="sml">Small molecule table (v1,v2)</option>
39 <option value="smf">Small molecule feature table (v2)</option>
40 <option value="sme">Small molecule evidence table (v2)</option>
41 </param>
42 </inputs>
43 <outputs>
44 <expand macro="output" type="mtd" label="Metadata"/>
45 <expand macro="output" type="prt" label="Proteins"/>
46 <expand macro="output" type="pep" label="Peptides"/>
47 <expand macro="output" type="psm" label="Peptide spectrum matches"/>
48 <expand macro="output" type="sml" label="Small molecules"/>
49 <expand macro="output" type="smf" label="Small molecule feature"/>
50 <expand macro="output" type="sme" label="Small molecule evidence"/>
51 </outputs>
52 <tests>
53 <test expect_num_outputs="5">
54 <param name="path_in" ftype="mztab" value="1.mztab"/>
55 <param name="out_select" value="mtd,prt,pep,psm,sml"/>
56 <output name="out_mtd" ftype="tabular">
57 <assert_contents><has_text text="mzTab-version"/></assert_contents>
58 </output>
59 <output name="out_prt" ftype="tabular">
60 <assert_contents><has_text text="accession"/></assert_contents>
61 </output>
62 <output name="out_pep" ftype="tabular">
63 <assert_contents><has_text text="&quot;&quot;"/></assert_contents>
64 </output>
65 <output name="out_psm" ftype="tabular">
66 <assert_contents><has_text text="PSM_ID"/></assert_contents>
67 </output>
68 <output name="out_sml" ftype="tabular">
69 <assert_contents><has_text text="&quot;&quot;"/></assert_contents>
70 </output>
71 </test>
72 <test expect_num_outputs="4">
73 <param name="path_in" ftype="mztab" value="2.mztab"/>
74 <param name="out_select" value="mtd,sml,smf,sme"/>
75 <output name="out_mtd" ftype="tabular">
76 <assert_contents><has_text text="mzTab-version"/></assert_contents>
77 </output>
78 <output name="out_sml" ftype="tabular">
79 <assert_contents><has_text text="SML_ID"/></assert_contents>
80 </output>
81 <output name="out_smf" ftype="tabular">
82 <assert_contents><has_text text="SMF_ID"/></assert_contents>
83 </output>
84 <output name="out_sme" ftype="tabular">
85 <assert_contents><has_text text="SME_ID"/></assert_contents>
86 </output>
87 </test>
88 </tests>
89 <help><![CDATA[
90 Convert a mztab or mztab2 file to tabular files using the pyteomics library https://pyteomics.readthedocs.io/en/latest/.
91
92 The specifications of the mztab and mztab2 formats can be found here https://github.com/HUPO-PSI/mzTab/.
93 ]]></help>
94 <citations>
95 <citation type="doi">10.1007/s13361-012-0516-6</citation>
96 <citation type="doi">10.1021/acs.jproteome.8b00717</citation>
97 </citations>
98 </tool>