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comparison PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml @ 0:c3f0b3a6339e draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 01:47:48 +0000
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-1:000000000000 0:c3f0b3a6339e
1 <tool id="pdaug_tsvtofasta" name="PDAUG TSVtoFASTA" version="0.1.0">
2
3 <description>Converts tabular peptide sequence data into fasta format</description>
4
5 <requirements>
6 <requirement type="package" version="0.24.2">pandas</requirement>
7 <requirement type="package" version="4.1.2">modlamp</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1" level="fatal" />
11 </stdio>
12 <command detect_errors="exit_code"><![CDATA[
13
14 python '$__tool_directory__/PDAUG_TSVtoFASTA.py' -I '$InFile' -M '$Method'
15
16 #if $Method == 'WithClassLabel'
17 -P '$OutFile1'
18 -N '$OutFile2'
19 #end if
20
21 #if $Method == 'NoClassLabel'
22 -O '$OutFile3'
23 #end if
24
25 ]]></command>
26
27 <inputs>
28 <param name="InFile" type="data" label="Input file" format="tabular" argument= "--InFile1" help="Input tabular file"/>
29 <param name="Method" type="select" label="Data conversion" argument="--Method" help="Split file if class labels are present" >
30 <option value="WithClassLabel"> WithClassLabel </option>
31 <option value="NoClassLabel" selected="true" > NoClassLabel </option>
32 </param>
33 </inputs>
34
35 <outputs>
36 <data name='OutFile1' format='fasta' label="${tool.name} on $on_string - ${Method} (tabular)" >
37 <filter>Method == "WithClassLabel"</filter>
38 </data>
39
40 <data name='OutFile2' format='fasta' label="${tool.name} on $on_string - ${Method} (tabular)">
41 <filter>Method == "WithClassLabel"</filter>
42 </data>
43
44 <data name='OutFile3' format='fasta' label="${tool.name} on $on_string - ${Method} (tabular)" >
45 <filter>Method == "NoClassLabel"</filter>
46 </data>
47 </outputs>
48 <tests>
49 <test>
50 <param name="InFile" value="test1.tsv"/>
51 <param name="Method" value="WithClassLabel"/>
52 <output name="OutFile1" file="test1/Positive.fasta"/>
53 <output name="OutFile2" file="test1/Negative.fasta"/>
54 </test>
55 <test>
56 <param name="InFile" value="test2.tsv"/>
57 <param name="Method" value="NoClassLabel"/>
58 <output name="OutFile3" file="test2/Out.fasta"/>
59 </test>
60 </tests>
61 <help><![CDATA[
62 .. class:: infomark
63
64 **What it does**
65
66 This tool converts tabular files into fasta file and split fasta file on the basis of the class label.
67
68 -----
69
70 **Inputs**
71 * **--InFile** Takes input as Tabular file with or without label.
72
73 -----
74
75 **Outputs**
76 * Returns fasta file.]]></help>
77 <citations>
78 <citation type="bibtex">
79 @misc{PDAUGGITHUB,
80 author = {Joshi, Jayadev and Blankenberg, Daniel},
81 year = {2020},
82 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
83 publisher = {GitHub},
84 journal = {GitHub repository},
85 url =
86 {https://github.com/jaidevjoshi83/pdaug.git},
87 }
88 </citation>
89 </citations>
90 </tool>
91
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93