Mercurial > repos > jay > pdaug_peptide_ngrams
diff PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.xml @ 0:7557b48b2872 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:10:12 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.xml Wed Oct 28 02:10:12 2020 +0000 @@ -0,0 +1,76 @@ +<tool id="pdaug_peptide_ngrams" name="PDAUG Peptide Ngrams" version="0.1.0" python_template_version="2.7"> + <description>Counts n-grams in the entire sequence set and fitting their distribution with the power-law distribution (Zipf’s law)</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[ + + python2 '$__tool_directory__/PDAUG_Peptide_Ngrams.py' -f1 '$fasta1' -f2 '$fasta2' --OutFile 'out.png' + + ]]></command> + + <inputs> + <param name="fasta1" type="data" format="fasta" label="First fasta file" argument= "--fasta1" help="First fasta file"/> + <param name="fasta2" type="data" format="fasta" label="Second fasta file" argument= "--fasta2" help="First fasta file"/> + </inputs> + + <outputs> + <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/> + </outputs> + + <tests> + <test> + <param name="fasta1" value="test1.fasta"/> + <param name="fasta2" value="test2.fasta"/> + <output name="output2" file="out.png"/> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +This tool counts n-grams in the entire peptide sequence set and fitting their distribution with the power-law distribution (Zipf’s law) and plot the results. + +----- + +**Inputs** + * **--InFile** Takes fasta file as input with peptide sequences. + +----- + +**Outputs** + * Returns 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> + <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, Bogumił M. and Marciniak, Marta and Dyrka, Witold}, + year={2017} + } + </citation> +</citations> +</tool> + + +