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date Mon, 05 Jun 2023 02:52:57 +0000
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1 <tool id="edu.tamu.cpt.sar.sar_finder" name="SAR Finder" version="1.0">
2 <description>SAR Domain Finder</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 </expand>
8 <command detect_errors="aggressive"><![CDATA[
9 python '$__tool_directory__/SAR_finder.py'
10 '$fa'
11 --sar_min '$sar_min'
12 --sar_max '$sar_max'
13 --out_fa '$out_fa'
14 --out_gff3 '$out_gff3'
15 --out_stat '$out_stat'
16 ]]></command>
17 <inputs>
18 <param label="Multi FASTA File" name="fa" type="data" format="fasta"/>
19 <param label="SAR domain minimal size" name="sar_min" type="integer" value="15"/>
20 <param label="SAR domain maximum size" name="sar_max" type="integer" value="20"/>
21 </inputs>
22 <outputs>
23 <data format="tabular" name="out_stat" label="candidate_SAR_stats.tsv"/>
24 <data format="fasta" name="out_fa" label="candidate_SAR.fa"/>
25 <data format="gff3" name="out_gff3" label="candidate_SAR.gff3"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="fa" value="simple-proteins.fa"/>
30 <param name="sar_min" value="15"/>
31 <param name="sar_max" value="20"/>
32 <output name="out_stat" file="candidate_SAR_stats.tsv"/>
33 <output name="out_fa" file="candidate_SAR.fa"/>
34 <output name="out_gff3" file="candidate_SAR.gff3"/>
35 </test>
36 </tests>
37 <help><![CDATA[
38
39 **What it does**
40 A tool that analyzes the sequence within the first 50 residues of a protein for a weakly hydrophobic domain called Signal-Anchor-Release (aka SAR).
41 The tool finds proteins that contain a stretch (default 15-20 residues) of hydrophobic residues (Ile, Leu, Val, Phe, Tyr, Trp, Met, Gly, Ala, Ser) and
42 calculates the % Gly/Ala/Ser/Thr residues in the hydrophobic stretch. The net charge on the N-terminus is also displayed to aid in determining the
43 SAR orientation in the membrane.[2]
44
45 Definition: A Signal-Anchor-Release (SAR) domain is an N-terminal, weakly hydrophobic transmembrane region rich in Gly/Ala and/or Ser (and sometimes Thr) residues.
46 The SAR domain is sometimes found in phage lysis proteins, including endolysins and holins. The SAR domain can be released from the membrane in a proton
47 motive force-dependent manner. Known SAR domains in phage endolysins often have >50-60% Gly/Ala/Ser/Thr content. SAR endolysins are expected to have a net positive
48 charge on the N-terminus by the positive-inside rule.
49
50 **INPUT** --> Protein Multi FASTA
51
52 **OUTPUT** -->
53
54 * Multi FASTA with candidate proteins that pass the SAR domain criteria
55
56 * Tabular summary file that lists every subdomain fitting the criteria for each potential SAR domain-containing protein with the following: protein name/sequence/length, SAR length/start/sequence/end, individual and total GAST% content in SAR, and N-terminal sequence/net charge
57
58 * Multi GFF3 for unique candidate SAR domain-containing proteins
59
60 ]]></help>
61 <citations>
62 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
63 <citation type="doi">https://dx.doi.org/10.1016/bs.aivir.2018.09.003</citation>
64 <citation type="bibtex">
65 @unpublished{galaxyTools,
66 author = {C. Ross},
67 title = {CPT Galaxy Tools},
68 year = {2020-},
69 note = {https://github.com/tamu-cpt/galaxy-tools/}
70 }
71 </citation>
72 </citations>
73 </tool>