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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Wed, 12 Jan 2022 20:40:16 +0000 |
parents | ea405d064794 |
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<tool id="pdaug_aa_property_based_peptide_generation" name="PDAUG AA Property Based Peptide Generation" version="0.1.0"> <description>Generates peptide sequence library based on amino acid properties</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 '$__tool_directory__/PDAUG_AA_Property_Based_Peptide_Generation.py' '$SelLibGene.LibGene' #if $SelLibGene.LibGene == 'Random' --seq_num '$SelLibGene.seq_num' --lenmin_s '$SelLibGene.lenmin_s' --lenmax_s '$SelLibGene.lenmax_s' --S_proba '$SelLibGene.S_proba' #end if #if $SelLibGene.LibGene == 'Helices' --seq_num '$SelLibGene.seq_num' --lenmin_s '$SelLibGene.lenmin_s' --lenmax_s '$SelLibGene.lenmax_s' #end if #if $SelLibGene.LibGene == 'Kinked' --seq_num '$SelLibGene.seq_num' --lenmax_s '$SelLibGene.lenmax_s' --lenmin_s '$SelLibGene.lenmin_s' #end if #if $SelLibGene.LibGene == 'Oblique' --seq_num '$SelLibGene.seq_num' --lenmax_s '$SelLibGene.lenmax_s' --lenmin_s '$SelLibGene.lenmin_s' #end if #if $SelLibGene.LibGene == 'Centrosymmetric' --seq_num '$SelLibGene.seq_num' --lenmax_s '$SelLibGene.lenmax_s' --lenmin_s '$SelLibGene.lenmin_s' #end if #if $SelLibGene.LibGene == 'HelicesACP' --seq_num '$SelLibGene.seq_num' --lenmax_s '$SelLibGene.lenmax_s' --lenmin_s '$SelLibGene.lenmin_s' #end if #if $SelLibGene.LibGene == 'Hepahelices' --seq_num '$SelLibGene.seq_num' --lenmax_s '$SelLibGene.lenmax_s' --lenmin_s '$SelLibGene.lenmin_s' #end if #if $SelLibGene.LibGene == 'AMPngrams' --seq_num '$SelLibGene.seq_num' --n_min '$SelLibGene.n_max' --n_max '$SelLibGene.n_min' #end if #if $SelLibGene.LibGene == 'AmphipathicArc' --seq_num '$SelLibGene.seq_num' --lenmax_s '$SelLibGene.lenmax_s' --lenmin_s '$SelLibGene.lenmin_s' --arcsize '$SelLibGene.arcsize' --hyd_gra '$SelLibGene.hydgra' #end if #if $SelLibGene.LibGene == 'MixedLibrary' --seq_num '$SelLibGene.seq_num' --centrosymmetric '$SelLibGene.centrosymmetric' --centroasymmetric '$SelLibGene.centroasymmetric' --helix '$SelLibGene.helix' --kinked '$SelLibGene.kinked' --oblique '$SelLibGene.oblique' --rand '$SelLibGene.rand' --randAMP '$SelLibGene.randAMP' --randAMPnoCM '$SelLibGene.randAMPnoCM' #end if --OutFasta '$output1' ]]></command> <inputs> <conditional name='SelLibGene' > <param name="LibGene" type="select" label="Methods to generate peptide sequence" argument=""> <option value="AmphipathicArc">AmphipathicArc Peptides</option> <option value="AMPngrams">AMPngrams Peptides</option> <option value="Centrosymmetric">Centrosymmetric Peptides</option> <option value="Helices">Helices Peptides</option> <option value="HelicesACP">HelicesACP Peptides</option> <option value="Hepahelices">Hepahelices Peptides</option> <option value="Kinked">Kinked Peptides</option> <option value="Oblique">Oblique Peptides</option> <option value="Random">Random Peptides</option> <option value="MixedLibrary">MixedLibrary Peptides</option> </param> <when value="Random"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> <param name="S_proba" type="float" value="1.0" label="Probability" argument="--S_proba" help="AA probability to be used to generate sequences." /> </when> <when value="Helices"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> </when> <when value="Kinked"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> </when> <when value="Oblique"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> </when> <when value="Centrosymmetric"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> <param name="symmetry_s" type="select" label="Symmetry" argument="--symmetry_s" help="Type of centrosymmetric sequences. symmetric: builds sequences out of only one block, asymmetric: builds sequences out of different blocks."> <option value="asymmetric">asymmetric</option> <option value="symmetric" >symmetric</option> </param> </when> <when value="HelicesACP"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> </when> <when value="Hepahelices"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> </when> <when value="AMPngrams"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="n_min" type="integer" value="3" label="Minimum length" argument="--n_min_s" help="Minimum length of generated peptides." /> <param name="n_max" type="integer" value="1" label="Maximum length" argument="--n_max_s" help="Maximum length of generated peptides."/> </when> <when value="AmphipathicArc"> <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> <param name="arcsize" type="integer" value="180" label="Arc size" argument="--arcsize" help="Arc size to choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture."/> <param name="hydgra" type="boolean" value="false" argument="--hyd_gra" label="Hydrophobic gradient" help="Method to mutate the generated sequences to have a hydrophobic gradient by substituting the last third of the sequence amino acids to hydrophobic."/> </when> <when value="MixedLibrary"> <param name="seq_num" type="integer" value="1000" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> <param name="centrosymmetric" type="integer" value="5" label="Ratio of symmetric centrosymmetric sequences in the library" argument="--lenmin_s" help="Ratio of symmetric centrosymmetric sequences in the library"/> <param name="centroasymmetric" type="integer" value="5" label="Ratio of asymmetric centrosymmetric sequences" help="Ratio of asymmetric centrosymmetric sequences in the library"/> <param name="helix" type="integer" value="3" label="Ratio of asymmetric centrosymmetric sequences" help="Ratio of asymmetric centrosymmetric sequences in the library"/> <param name="kinked" type="integer" value="3" label="Ratio of kinked" help="Ratio of kinked amphipathic helical sequences in the library"/> <param name="oblique" type="integer" value="2" label="Ratio of oblique" help="Ratio of oblique oriented amphipathic helical sequences in the library"/> <param name="rand" type="integer" value="10" label="Ratio of random sequneces" help="Ratio of random sequneces in the library"/> <param name="randAMP" type="integer" value="10" label="Ratio of random sequences with APD2 amino acid distribution" help="Ratio of random sequences with APD2 amino acid distribution in the library"/> <param name="randAMPnoCM" type="integer" value="5" label="Ratio of random sequences with APD2 amino acid distribution without Cys and Met in the library" help="Ratio of random sequences with APD2 amino acid distribution in the library"/> </when> </conditional> </inputs> <outputs> <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelLibGene.LibGene} (fasta)" /> </outputs> <tests> <test> <param name="LibGene" value="Random"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <param name="S_proba" value="1.0" /> <output name='output1' file="Out1.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="Helices"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <output name='output1' file="Out2.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="Kinked"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <output name='output1' file="Out3.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="Oblique"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <output name='output1' file="Out4.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="Centrosymmetric"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <param name="symmetry_s" value="asymmetric" /> <output name='output1' file="Out5.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="HelicesACP"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <output name='output1' file="Out6.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="Hepahelices"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <output name='output1' file="Out7.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="AMPngrams"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <output name='output1' file="Out8.fasta" lines_diff='20' /> </test> <test> <param name="LibGene" value="AmphipathicArc"/> <param name="seq_num" value="5" /> <param name="lenmin_s" value="7" /> <param name="lenmax_s" value="21" /> <param name="arcsize" value="180" /> <param name="hydgra" value="false" /> <output name='output1' file="Out9.fasta" lines_diff='20' /> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This module incorporates different classes to generate peptide sequences with different characteristics from scratch. The following classes are available Random, Helices, Kinked, Oblique, Centrosymmetric, AmphipathicArc, HelicesACP, MixedLibrary, Hepahelices, and AMPngrams. * **Random** Generates random sequences with a specified amino acid distribution. * **Helices** Generate presumed amphipathic helical sequences with a hydrophobic moment. * **Kinked** Generates presumed amphipathic helices with a kink (Pro residue). * **Oblique** Generates presumed oblique oriented sequences in presence of lipid membranes. * **Centrosymmetric** Generates centrosymmetric sequences with a symmetry axis. * **AmphipathicArc** Generates presumed amphipathic helices with controlled hydrophobic arc size. * **HelicesACP** Generates sequences with the amino acid probability of helical ACPs. * **MixedLibrary** Generates a mixed library of sequences of most other classes. * **Hepahelices** Generates presumed amphipathic helices with a heparin-binding-domain. * **AMPngrams** Generates sequences from most frequent ngrams in the APD3. ----- **Inputs** **1** Random Peptides * **--seq_num** Number of sequences to be generated. * **--lenmin_s** Peptide minimum legnth. * **--lenmax_s** Peptide maximum legnth. * **--S_proba** AA probability to be used to generate sequences. Available from str: AMP, AMPnoCM, rand, randnoCM. You can also provide your own list of porbabilities as a list (in AA order, length 20, sum to 1) **2** Helice Peptides * **--seq_num** Number of sequence to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum length. **3** Kinked Peptides * **--seq_num** Number of sequences to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum length. **4** Obliqu Peptides * **--seq_num** Number of sequence to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum length. **5** Centrosymmetric Peptides * **--seq_num** Number of sequences to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum length. * **--symmetry_s** symmetry type of centrosymmetric sequences. symmetric: builds sequences out of only one block, asymmetric: builds sequences out of different blocks **6** HelicesACP Peptides * **--seq_num** Number of sequences to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum length. **7** Hepahelices Peptides * **--seq_num** Number of sequences to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum length. **7** AMPngrams Peptides * **--seq_num** Number of sequence to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum length. **9** AmphipathicArc Peptides * **--seq_num** Number of sequence to be generated. * **--lenmin_s** Peptide minimum length. * **--lenmax_s** Peptide maximum lenngth. * **--arcsize** Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture **10** MixedLibrary Peptides * **Todo** ----- **Outputs** * 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> <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>