Mercurial > repos > jay > pdaug_sequence_similarity_network

comparison PDAUG_Sequence_Network/PDAUG_Sequence_Network.xml @ 0:e650de82bcc7 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 01:50:00 +0000
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1 <tool id="pdaug_sequence_similarity_network" name="PDAUG Sequence Similarity Network" version="0.1.0" python_template_version="3.6">
2 <description>Generates a sequence similarity network</description>
3
4 <requirements>
5 <requirement type="package" version="0.12.0">python-Levenshtein</requirement>
6 <requirement type="package" version="3.2.2">matplotlib</requirement>
7 <requirement type="package" version="2.5">networkx</requirement>
8 </requirements>
9
10 <command detect_errors="exit_code"><![CDATA[
11
12 python '$__tool_directory__/PDAUG_Sequence_Network.py' --InFile '$input1' --OutFile 'out.png'
13 ]]></command>
14
15 <inputs>
16 <param name="input1" type="data" format="fasta" label="Input fasta file" argument= "--InFile" help="Input fasta file with peptides"/>
17
18 </inputs>
19
20 <outputs>
21 <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png" />
22
23 </outputs>
24
25 <tests>
26 <test>
27 <param name="input1" value="positive.fasta"/>
28 <output name="output2" file="out.png" compare="sim_size" delta="10000" />
29 </test>
30 </tests>
31
32 <help><![CDATA[
33 .. class:: infomark
34
35 **What it does**
36
37 This tool calculates Levenshtein distance between peptide sequences and plots the data in the form of a sequence similarity network.
38
39 -----
40
41 **Inputs**
42 * **--InFile** Takes peptide sequences as fasta file.
43
44 -----
45
46 **Outputs**
47 * Return html report file.]]></help>
48 <citations>
49 <citation type="bibtex">
50 @misc{PDAUGGITHUB,
51 author = {Joshi, Jayadev and Blankenberg, Daniel},
52 year = {2020},
53 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
54 publisher = {GitHub},
55 journal = {GitHub repository},
56 url =
57 {https://github.com/jaidevjoshi83/pdaug.git},
58 }
59 </citation>
60 </citations>
61 </tool>
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