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comparison parse_mito_blast.xml @ 0:f172b1f77d6c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
author iuc
date Thu, 12 May 2022 10:45:45 +0000
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1 <tool id="parse_mito_blast" name="Parse mitochondrial blast" version="@TOOL_VERSION@" profile="21.05">
2 <description>overlap-conscious coverage calculation between scaffold-accession number pairs from blast output</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.1</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">parse_mito_blast</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 parse_mito_blast.py
11 --blastout '$blastout'
12 ]]>
13 </command>
14 <inputs>
15 <param argument="blastout" type="data" format="tabular" label="Tabular file generated by mito-blast"/>
16 </inputs>
17 <outputs>
18 <data name="cov_report" format="tabular" from_work_dir="cov_report.tsv" label="${tool.name} on ${on_string}" />
19 <data name="mito_scaff_names" format="txt" from_work_dir="mito_scaff_names.txt" label="contaminant scaffolds on ${on_string}" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="blastout" value="test_input.tsv" />
24 <output name="cov_report" file="test_cov_report.tsv" ftype="tabular" />
25 <output name="mito_scaff_names" file="test_mito_scaff_names.txt" ftype="txt" />
26 </test>
27 </tests>
28 <help><![CDATA[
29
30 This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output \
31 all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
32 collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
33 account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
34 sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold /
35 (sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
36 identity to a mitochondrial subject sequence. To use, pass a format 6 blast output (--blastout) and the desired name of the report.
37
38 NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' /
39 and will be sensitive to this order.
40 ]]>
41 </help>
42 <citations>
43 <citation type="bibtex">
44 @misc{Danecek_et_al,
45 Author={Danecek, P., Schiffels, S., Durbin, R.},
46 title={Multiallelic calling model in bcftools (-m)},
47 url = {http://samtools.github.io/bcftools/call-m.pdf},}
48 </citation>
49 </citations>
50 </tool>