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author | cpt |
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date | Fri, 17 Jun 2022 12:24:06 +0000 |
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<?xml version="1.1"?> <tool id="edu.tamu.cpt2.phage.disruptin_prox" name="Disruptin Proximity to Lysis Genes Tool" version="1.1"> <description>identifies lysis gene candidates close to genes encoding endolysin domains and genes encoding transmembrane domains</description> <macros> <import>macros.xml</import> <import>cpt-macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="3.0.2">intervaltree</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ python $__tool_directory__/disruptin_proximity_2_lysis_genes.py $lgc $tmhmm $ipro $genome $window $enzyme --oa $oa --ob $ob --oc $oc --od $od ]]></command> <inputs> <param label="Lysis Gene Candidates" name="lgc" type="data" format="fasta" /> <param label="TMHMM Results" name="tmhmm" type="data" format="gff3" /> <param label="InterProScan Results" name="ipro" type="data" format="gff3" /> <param label="Phage Genome" name="genome" type="data" format="gff3" /> <param label="Adjacency Window Size" name="window" type="integer" value="1000" /> <param label="Enzyme Domain List" name="enzyme" type="data" format="tabular" /> </inputs> <outputs> <data format="gff3" name="oa" label="Protein with endolysin-associated domain and adjacent to lysis gene candidate"/> <data format="gff3" name="ob" label="Lysis gene candidates near possible endolysin"/> <data format="gff3" name="oc" label="Protein with transmembrane domain and adjacent to lysis gene candidate"/> <data format="gff3" name="od" label="Lysis gene candidates near TMD-containing protein"/> </outputs> <help><![CDATA[ **What it does** This program is intended to identify protein coding sequences within a certain window (number of base pairs) of genes encoding recognized endolysin domains and others encoding transmembrane domains. The goal is to identify possible lysis genes or to narrow a list of disruptin candidates. ]]></help> <citations> <citation type="doi">10.1371/journal.pcbi.1008214</citation> <citation type="bibtex"> @unpublished{galaxyTools, author = {A. Holt}, title = {CPT Galaxy Tools}, year = {2020}, note = {https://github.com/tamu-cpt/galaxy-tools/} } </citation> </citations> </tool>