Mercurial > repos > jay > pdaug_peptide_core_descriptors
diff PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.xml @ 0:0fc091fb7e8f draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:12:57 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.xml Wed Oct 28 02:12:57 2020 +0000 @@ -0,0 +1,78 @@ +<tool id="pdaug_peptide_core_descriptors" name="PDAUG Peptide Core Descriptors" version="0.1.0"> + <description>Calculates core descriptors of peptide sequences</description> + + <requirements> + <requirement type="package" version="0.24.2">pandas</requirement> + <requirement type="package" version="4.2.1">modlamp</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + + python '$__tool_directory__/PDAUG_Peptide_Core_Descriptors.py' -I '$input1' -N '$ngrams' -O '$output1' + + ]]></command> + + <inputs> + <param name="input1" type="data" label="Input file" format="fasta" argument= "--InFile1" help="Input fasta file with peptides"/> + <param name="ngrams" type="integer" label="ngram size" value="3" help="ngram size"/> + </inputs> + + <outputs> + <data name='output1' format='tabular' label="${tool.name} on $on_string - n-grams (tabular)" /> + </outputs> + <tests> + <test> + <param name="input1" value="test.fasta"/> + <param name="ngrams" value="3" /> + <output name="output1" file="Out.tsv"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Calculates the frequency of ngrames in peptide sequences. + +----- + +**Inputs** + * **--InFile** Fasta file with peptide sequences as Input File. + * **--Ngrams** Integer value of Ngrams frequency to be calculated. + +----- + +**Outputs** + * **--OutFile** Returns tabular data 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{müller_gabernet_hiss_schneider_2017, + title={modlAMP: Python for antimicrobial peptides}, + volume={33}, + DOI={10.1093/bioinformatics/btx285}, + number={17}, + journal={Bioinformatics}, + author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, + year={2017}, + pages={2753–2755} + } + </citation> +</citations> +</tool> + + +