Mercurial > repos > jay > pdaug_uversky_plot
diff PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.xml @ 0:070fc1da6df7 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:56:46 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.xml Wed Oct 28 01:56:46 2020 +0000 @@ -0,0 +1,78 @@ +<tool id="pdaug_uversky_plot" name="PDAUG Uversky Plot" version="0.1.0" python_template_version="3.6"> + <description>Uversky plot to analyze ordered and disordered proteins</description> + + <requirements> + <requirement type="package" version="2.7.18">python</requirement> + <requirement type="package" version="1.4.6">powerlaw</requirement> + <requirement type="package" version="0.2.4">quantiprot</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + + python '$__tool_directory__/PDAUG_Uversky_Plot.py' --Fasta1 '$input1' --Fasta2 '$input2' --OutFile 'out.png' + + ]]></command> + + <inputs> + <param name="input1" type="data" format="fasta" label="First fasta file" argument= "--Fasta1" help="First fasta file with Peptides"/> + <param name="input2" type="data" format="fasta" label="Second fasta file" argument="--Fasta2" help="Second fasta file with Peptides"/> + </inputs> + + <outputs> + <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/> + </outputs> + + <tests> + <test> + <param name="input1" value="test1.fasta"/> + <param name="input2" value="test2.fasta"/> + <output name="output2" file="out.png"/> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +This plot divides analyze peptide sequences on globular and IDP subsets based on their mean net charge versus mean hydropathy. The line represents the permeable boundary between both subsets. + +----- + +**Inputs** + * **--Fasta1** The first fasta file. + * **--Fasta2** The second fasta file. + +----- + +**Outputs** + * Return html 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> + + <citation type="bibtex"> + @article{konopka_marciniak_dyrka_2017, + title={Quantiprot - a Python package for quantitative analysis of protein sequences}, + volume={18}, + DOI={10.1186/s12859-017-1751-4}, + number={1}, + journal={BMC Bioinformatics}, + author={Konopka, BogumiĆ M. and Marciniak, Marta and Dyrka, Witold}, + year={2017} + } + </citation> +</citations> +</tool> + + +