Mercurial > repos > jay > pdaug_sequence_based_peptide_generation
view PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.xml @ 2:cda6264267f7 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 8b18552f6d2b2261efebe1075ff4c18a295b94dd"
author | jay |
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date | Tue, 29 Dec 2020 19:00:54 +0000 |
parents | 93f7668caa55 |
children | dd21da1ac55c |
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<tool id="pdaug_sequence_based_peptide_generation" name="PDAUG Sequence Based Peptide Generation" version="0.1.0"> <description>Generates peptide sequence library</description> <requirements> <requirement type="package" version="0.24.2">pandas</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/PDAUG_Sequence_Based_Peptide_Generation.py' '$SelMethod.Method' --outputFile '$output1' #if $SelMethod.Method == 'MutatedPeptides' --sequence '$SelMethod.input1' --mutation_site_list '$SelMethod.mutation_site_list' --AA_list '$SelMethod.AA_list' #end if #if $SelMethod.Method == 'RandomPeptides' --AA_list '$SelMethod.AA_list' --pep_length '$SelMethod.pep_length' --out_pep_lenght '$SelMethod.out_pep_length' #end if #if $SelMethod.Method == 'SlidingWindowPeptide' --InFile '$SelMethod.input1' --winSize '$SelMethod.WinSize' --FragSize '$SelMethod.FragSize' #end if ]]></command> <inputs> <conditional name='SelMethod' > <param name="Method" type="select" label="Methods to generate peptides " argument=""> <option value="MutatedPeptides">MutatedPeptides</option> <option value="RandomPeptides">RandomPeptides</option> <option value="SlidingWindowPeptide">SlidingWindowPeptide</option> </param> <when value="MutatedPeptides"> <param name="input1" type="text" label="Peptide sequence" value="KLLKLLKKKLLK" argument= "--sequence" help="Peptide sequence"/> <param name="mutation_site_list" label="Mutation Site" value="2" type="text" argument="--mutation_site_list" help="List of integer to introduce mutation"/> <param name="AA_list" type="text" label="Amino Acide List" value="I,H" argument="-AA_list" help="List of amino acids to be replaced"/> </when> <when value="RandomPeptides"> <param name="AA_list" type="text" label="Amino Acide List" value="G,L,F,D,I,V,K" argument="-AA_list" help="List of amino acids" /> <param name="pep_length" type="integer" optional="false" label="Peptide Legnth" value="7" argument="--pep_length" help="Length of output peptide"/> <param name="out_pep_length" type="integer" optional="false" label="Nomber of peptides" value="7" argument="--out_pep_length" help="Number of peptides to be generated"/> </when> <when value="SlidingWindowPeptide"> <param name="input1" type="data" label="Input Sequence" format="fasta" argument= "--InFile" help="Input protein sequence"/> <param name="WinSize" type="integer" label="Window Size" value="3" argument="--winSize" help="Sliding window size" /> <param name="FragSize" type="integer" label="Fragment Size" value="7" argument="--FragSize" help="Size of the peptides" /> </when> </conditional> </inputs> <outputs> <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelMethod.Method} (fasta)" /> </outputs> <tests> <test> <param name='Method' value="MutatedPeptides" /> <param name='input1' value="KLLKLLKKKLLK" /> <param name='mutation_site_list' value="2" /> <param name='AA_list' value="G,Y" /> <output name="output1" file="out1.fasta" /> </test> <test> <param name='Method' value="RandomPeptides" /> <param name='AA_list' value="G,L,F,D,I,V,K," /> <param name='pep_length' value="7" /> <param name='out_pep_length' value="7" /> <output name="output1" file="out2.fasta" lines_diff='28'/> </test> <test> <param name='Method' value="SlidingWindowPeptide" /> <param name='input1' value="test1.fasta" /> <param name='WinSize' value="3" /> <param name='FragSize' value="7" /> <output name="output1" file="out3.fasta" /> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool generates peptide sequences based on three sequences based properties which includes Mutated Peptides, Random Peptides, and Sliding Window Peptide. ----- **Inputs** **1** MutatedPeptides * **--sequence** Input peptide sequence * **--mutation_site_list** Sites to mutated AA as Integer values * **--AA_list** List of amino acids to replace **2** RandomPeptides * **--AA_list** List of amino acids * **--pep_length** Length of peptide sequences * **--out_pep_lenght** Number of output peptides **3** SlidingWindowPeptide * **--InFile** Input protein sequences fasta file * **--winSize** Sliding window size * **--FragSize** Output Peptide sequence size ----- **Outputs** * **--outputFile** Returns fasta files with peptide sequences. ]]></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>