Mercurial > repos > cpt > cpt_blast_to_xmfa
comparison cpt_blast_to_xmfa/blast2pxmfa.xml @ 0:84761ea60231 draft
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author | cpt |
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date | Fri, 01 Jul 2022 13:36:11 +0000 |
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1 <?xml version="1.0"?> | |
2 <tool id="edu.tamu.cpt.blast.blast2pxmfa" name="Blast TSV to Protein XMFA" version="1.0"> | |
3 <description></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="2.1">clustalw</requirement> | |
10 </expand> | |
11 <command detect_errors="aggressive"><![CDATA[ | |
12 $__tool_directory__/blast2pxmfa.py | |
13 @BLAST_TSV@ | |
14 $fasta | |
15 $gff3 | |
16 $output | |
17 ]]></command> | |
18 <inputs> | |
19 <expand macro="blast_tsv" /> | |
20 <expand macro="gff3_with_fasta" /> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="pxmfa" name="output"/> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="blast_tsv" value="results.tsv"/> | |
28 <param name="fasta" value="related.fa"/> | |
29 <param name="gff3" value="related.gbk.gff"/> | |
30 <output name="output" file="cbk.xmfa"> | |
31 <assert_contents> | |
32 <has_n_lines n="7547" delta="100"/> | |
33 </assert_contents> | |
34 </output> | |
35 </test> | |
36 </tests> | |
37 <help><![CDATA[ | |
38 .. class:: warningmark | |
39 | |
40 You likely should first filter your data first using the `Blast Tabular Dice | |
41 Filter tool <root?tool_id=edu.tamu.cpt.blast.blasttab_dice_filter>`__. | |
42 | |
43 **What it does** | |
44 | |
45 This tool processes BLAST Tabular results into a *protein* XMFA file. This | |
46 permits visualizing the data with CPT developed XMFA based tooling. | |
47 | |
48 **How it works** | |
49 | |
50 The tool works by: | |
51 | |
52 - taking the set of blast results | |
53 - clustering them according to relationships detected by blast | |
54 - running ClustalW to generate a set of alignments for each cluster | |
55 - outputting those clusters in the XMFA format | |
56 ]]></help> | |
57 <citations> | |
58 </citations> | |
59 </tool> |