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date Fri, 10 Jun 2022 08:46:28 +0000
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1 <?xml version="1.0"?>
2 <tool id="edu.tamu.cpt.blast.relatedness.prot" name="Related Genomes" version="19.1.0.0">
3 <description>based on protein blast results</description>
4 <macros>
5 <import>macros.xml</import>
6 <import>cpt-macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="aggressive">
10 $__tool_directory__/relatedness_prot.py
11 ${blastIn.blast}
12 $__tool_directory__/TaxID_List.txt
13 --hits $hits
14 $filter
15 --protein
16 #if $blastIn.blastType == "XML":
17 --xmlMode
18 #end if
19 --taxFilter "$taxFilter"
20 > $accession_list
21 </command>
22 <inputs>
23 <conditional name="blastIn">
24 <param name="blastType" type="select" label="Blastn Input Type">
25 <option value="XML" selected="true">Blast XML</option>
26 <option value="TSV">Blast Tabular</option>
27 </param>
28 <when value="XML">
29 <param label="Blastn Results (Blast XML)" name="blast" type="data" format="blastxml"/>
30 </when>
31 <when value="TSV">
32 <param label="Blastn Results" name="blast" type="data" format="tsv,tabular"/>
33 </when>
34 </conditional>
35 <param label = 'Number of results to return' name="hits" type="integer" size="15" value="5"/>
36 <param name="filter" type="boolean" truevalue="" falsevalue="--noFilter" checked="true" label="Automatically filter by phage Taxonomy IDs"/>
37 <param name="taxFilter" type="text" label="TaxIDs to filter out of results (Space separated)"/>
38 </inputs>
39 <outputs>
40 <data format="tabular" name="accession_list" label="Top BlastP Hits" />
41 </outputs>
42 <tests>
43 <test>
44 <conditional name="blastIn">
45 <param name="blastType" value="TSV"/>
46 <param name="blast" value="prot_relate_in.tab"/>
47 </conditional>
48 <param name="hits" value="10"/>
49 <output name="accession_list" file="prot_relate_out.tab" lines_diff="4"/>
50 </test>
51 </tests>
52 <help>
53 **What it does**
54
55 This tool filters a set of BLASTp results and return the top
56 related genomes based on number of protein-protein matches. The
57 default mode is to only consider phage hits (based on TaxID),
58 but this can the toggled off.
59
60 The input must be a tabular file from a BLASTp run with the qseqID,
61 sallseqid, salltitles, sallacc, and staxIDs fields selected.
62
63 The output will be a tabular file with the top hits returned,
64 where each row specifies the TaxID, organism name, and number of
65 similar unique protein hits shared.
66 </help>
67 <expand macro="citations-2020" />
68 </tool>