Mercurial > repos > jay > pdaug_sequence_similarity_network
view PDAUG_Sequence_Network/PDAUG_Sequence_Network.xml @ 5:9012052b1dad draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
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date | Sun, 31 Jan 2021 02:00:07 +0000 |
parents | e650de82bcc7 |
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<tool id="pdaug_sequence_similarity_network" name="PDAUG Sequence Similarity Network" version="0.1.0" python_template_version="3.6"> <description>Generates a sequence similarity network</description> <requirements> <requirement type="package" version="0.12.0">python-Levenshtein</requirement> <requirement type="package" version="3.2.2">matplotlib</requirement> <requirement type="package" version="2.5">networkx</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Sequence_Network.py' --InFile '$input1' --OutFile 'out.png' ]]></command> <inputs> <param name="input1" type="data" format="fasta" label="Input fasta file" argument= "--InFile" help="Input fasta file with peptides"/> </inputs> <outputs> <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png" /> </outputs> <tests> <test> <param name="input1" value="positive.fasta"/> <output name="output2" file="out.png" compare="sim_size" delta="10000" /> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool calculates Levenshtein distance between peptide sequences and plots the data in the form of a sequence similarity network. ----- **Inputs** * **--InFile** Takes peptide sequences as fasta file. ----- **Outputs** * Return html report file.]]></help> <citations> <citation type="bibtex"> @misc{PDAUGGITHUB, author = {Joshi, Jayadev and Blankenberg, Daniel}, year = {2020}, title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/jaidevjoshi83/pdaug.git}, } </citation> </citations> </tool>