Mercurial > repos > cpt > cpt_disruptin_proximity
comparison cpt_disruptin_proximity/disruptin_proximity_2_lysis_genes.xml @ 0:6661bb42b5a9 draft
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author | cpt |
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date | Fri, 17 Jun 2022 12:24:06 +0000 |
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1 <?xml version="1.1"?> | |
2 <tool id="edu.tamu.cpt2.phage.disruptin_prox" name="Disruptin Proximity to Lysis Genes Tool" version="1.1"> | |
3 <description>identifies lysis gene candidates close to genes encoding endolysin domains and genes encoding transmembrane domains</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 <import>cpt-macros.xml</import> | |
7 </macros> | |
8 <expand macro="requirements"> | |
9 <requirement type="package" version="3.0.2">intervaltree</requirement> | |
10 </expand> | |
11 <command detect_errors="aggressive"><![CDATA[ | |
12 python $__tool_directory__/disruptin_proximity_2_lysis_genes.py | |
13 $lgc | |
14 $tmhmm | |
15 $ipro | |
16 $genome | |
17 $window | |
18 $enzyme | |
19 --oa $oa | |
20 --ob $ob | |
21 --oc $oc | |
22 --od $od | |
23 | |
24 ]]></command> | |
25 <inputs> | |
26 <param label="Lysis Gene Candidates" name="lgc" type="data" format="fasta" /> | |
27 <param label="TMHMM Results" name="tmhmm" type="data" format="gff3" /> | |
28 <param label="InterProScan Results" name="ipro" type="data" format="gff3" /> | |
29 <param label="Phage Genome" name="genome" type="data" format="gff3" /> | |
30 <param label="Adjacency Window Size" name="window" type="integer" value="1000" /> | |
31 <param label="Enzyme Domain List" name="enzyme" type="data" format="tabular" /> | |
32 </inputs> | |
33 <outputs> | |
34 <data format="gff3" name="oa" label="Protein with endolysin-associated domain and adjacent to lysis gene candidate"/> | |
35 <data format="gff3" name="ob" label="Lysis gene candidates near possible endolysin"/> | |
36 <data format="gff3" name="oc" label="Protein with transmembrane domain and adjacent to lysis gene candidate"/> | |
37 <data format="gff3" name="od" label="Lysis gene candidates near TMD-containing protein"/> | |
38 </outputs> | |
39 <help><![CDATA[ | |
40 **What it does** | |
41 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. | |
42 The goal is to identify possible lysis genes or to narrow a list of disruptin candidates. | |
43 | |
44 ]]></help> | |
45 <citations> | |
46 <citation type="doi">10.1371/journal.pcbi.1008214</citation> | |
47 <citation type="bibtex"> | |
48 @unpublished{galaxyTools, | |
49 author = {A. Holt}, | |
50 title = {CPT Galaxy Tools}, | |
51 year = {2020}, | |
52 note = {https://github.com/tamu-cpt/galaxy-tools/} | |
53 } | |
54 </citation> | |
55 </citations> | |
56 </tool> |