diff cpt_disruptin_proximity/disruptin_proximity_2_lysis_genes.xml @ 0:6661bb42b5a9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_disruptin_proximity/disruptin_proximity_2_lysis_genes.xml	Fri Jun 17 12:24:06 2022 +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+        @unpublished{galaxyTools, 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>