Mercurial > repos > jay > pdaug_peptide_core_functions
view PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml @ 2:0cd905083504 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 8b18552f6d2b2261efebe1075ff4c18a295b94dd"
author | jay |
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date | Tue, 29 Dec 2020 18:36:00 +0000 |
parents | 562dc0806625 |
children | 6822d43a5f84 |
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<tool id="pdaug_peptide_core_functions" name="PDAUG Peptide Core Functions" version="0.1.0"> <description> Peptide sequence related core functions </description> <requirements> <requirement type="package" version="0.24.2">pandas</requirement> <requirement type="package" version="4.1.2">modlamp</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Peptide_Core_Functions.py' '$SelCoreFunction.CoreFunction' --InFile '$InFile' #if $SelCoreFunction.CoreFunction == 'mutateAA' --nr '$SelCoreFunction.nr' --Prob '$SelCoreFunction.prob' #end if #if $SelCoreFunction.CoreFunction == 'filteraa' --FilterAA '$SelCoreFunction.FilterAA' #end if --FastOut '$output1' ]]></command> <inputs> <param name="InFile" type="data" format="fasta" label="Input file" argument= "--InFile" help="Input fasta file with peptides"/> <conditional name='SelCoreFunction' > <param name="CoreFunction" type="select" label="Analysis options" argument=""> <option value="mutateAA">Mutate Amino Acid</option> <option value="filterduplicates">Filter Duplicates</option> <option value="keepnaturalaa">Keep Naturalaa</option> <option value="filteraa">Filter Amino Acid</option> </param> <when value="mutateAA"> <param name="nr" type="integer" label="Number of mutations" value="3" argument="--nr" help="Number of mutations"/> <param name="prob" type="float" label="Probability" value="1.0" argument="--Prob" help="Probability of mutating a sequence" /> </when> <when value="filterduplicates"> </when> <when value="keepnaturalaa"> </when> <when value="filteraa"> <param name="FilterAA" type="text" value="eisenberg" label="Filter AA" argument="--FilterAA" help="Amino acids to be filtered" /> </when> </conditional> </inputs> <outputs> <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelCoreFunction.CoreFunction} (fasta)" /> </outputs> <tests> <test> <param name="InFile" value="test1.fasta"/> <param name="CoreFunction" value="mutateAA" /> <param name="nr" value="3"/> <param name="prob" value="1.0"/> <output name="output1" file="out1.fasta" lines_diff="2"/> </test> <test> <param name="InFile" value="test2.fasta"/> <param name="CoreFunction" value="filterduplicates" /> <output name="output1" file="out2.fasta" /> </test> <test> <param name="InFile" value="test3.fasta"/> <param name="CoreFunction" value="keepnaturalaa" /> <output name="output1" file="out3.fasta" /> </test> <test> <param name="InFile" value="test4.fasta"/> <param name="CoreFunction" value="filteraa" /> <param name="FilterAA" value="eisenberg" /> <output name="output1" file="out4.fasta" /> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool performs some core functions on the peptide sequences and equipped with various options * **Mutated Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly. * **Filter Duplicates** Method to filter duplicates in the sequences from the class attribute sequences. * **Keep Naturalaa** Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character. * **Filter Amino Acid** Method to filter out corresponding names and descriptor values of sequences with given amino acids in the argument list aminoacids. ----- **Inputs** 1 **Mutate Amino Acid** * **--InFile** takes Fasta file with peptide sequences. * **--nr** Number of mutations. * **--probability** Probability of mutating a sequence. 2 **Filter Duplicates*** * **--InFile** takes Fasta file with peptide sequences. 3 **Keep Naturalaa** * **--InFile** takes Fasta file with peptide sequences. 4 **Filter Amino Acid** * **--InFile** takes Fasta file with peptide sequences. ----- **Outputs** * Returns a fasta 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>