Mercurial > repos > cpt > cpt_disruptin_proximity
comparison disruptin_proximity_2_lysis_genes.xml @ 1:5081ba961953 draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt |
|---|---|
| date | Mon, 05 Jun 2023 02:40:58 +0000 |
| parents | |
| children | 16c3654c9dbb |
comparison
equal
deleted
inserted
replaced
| 0:6661bb42b5a9 | 1:5081ba961953 |
|---|---|
| 1 <tool id="edu.tamu.cpt2.phage.disruptin_prox" name="Disruptin Proximity to Lysis Genes Tool" version="1.1"> | |
| 2 <description>identifies lysis gene candidates close to genes encoding endolysin domains and genes encoding transmembrane domains</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 <import>cpt-macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"> | |
| 8 <requirement type="package" version="3.0.2">intervaltree</requirement> | |
| 9 </expand> | |
| 10 <command detect_errors="aggressive"><![CDATA[ | |
| 11 python '$__tool_directory__/disruptin_proximity_2_lysis_genes.py' | |
| 12 '$lgc' | |
| 13 '$tmhmm' | |
| 14 '$ipro' | |
| 15 '$genome' | |
| 16 '$window' | |
| 17 '$enzyme' | |
| 18 --oa '$oa' | |
| 19 --ob '$ob' | |
| 20 --oc '$oc' | |
| 21 --od '$od' | |
| 22 | |
| 23 ]]></command> | |
| 24 <inputs> | |
| 25 <param label="Lysis Gene Candidates" name="lgc" type="data" format="fasta"/> | |
| 26 <param label="TMHMM Results" name="tmhmm" type="data" format="gff3"/> | |
| 27 <param label="InterProScan Results" name="ipro" type="data" format="gff3"/> | |
| 28 <param label="Phage Genome" name="genome" type="data" format="gff3"/> | |
| 29 <param label="Adjacency Window Size" name="window" type="integer" value="1000"/> | |
| 30 <param label="Enzyme Domain List" name="enzyme" type="data" format="tabular"/> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="gff3" name="oa" label="Protein with endolysin-associated domain and adjacent to lysis gene candidate"/> | |
| 34 <data format="gff3" name="ob" label="Lysis gene candidates near possible endolysin"/> | |
| 35 <data format="gff3" name="oc" label="Protein with transmembrane domain and adjacent to lysis gene candidate"/> | |
| 36 <data format="gff3" name="od" label="Lysis gene candidates near TMD-containing protein"/> | |
| 37 </outputs> | |
| 38 <help><![CDATA[ | |
| 39 **What it does** | |
| 40 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. | |
| 41 The goal is to identify possible lysis genes or to narrow a list of disruptin candidates. | |
| 42 | |
| 43 ]]></help> | |
| 44 <citations> | |
| 45 <citation type="doi">10.1371/journal.pcbi.1008214</citation> | |
| 46 <citation type="bibtex"> | |
| 47 @unpublished{galaxyTools, | |
| 48 author = {A. Holt}, | |
| 49 title = {CPT Galaxy Tools}, | |
| 50 year = {2020}, | |
| 51 note = {https://github.com/tamu-cpt/galaxy-tools/} | |
| 52 } | |
| 53 </citation> | |
| 54 </citations> | |
| 55 </tool> |