Mercurial > repos > iuc > parse_mito_blast

annotate parse_mito_blast.xml @ 1:3c9ad4adf8d2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 9c9689f095805b738f654eed152900339753f6fd
author iuc
date Thu, 09 Jun 2022 18:07:51 +0000
parents f172b1f77d6c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3c9ad4adf8d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 9c9689f095805b738f654eed152900339753f6fd
iuc
parents: 0
diff changeset
1 <tool id="parse_mito_blast" name="Parse mitochondrial blast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
0
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
2 <description>overlap-conscious coverage calculation between scaffold-accession number pairs from blast output</description>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
3 <macros>
1
3c9ad4adf8d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 9c9689f095805b738f654eed152900339753f6fd
iuc
parents: 0
diff changeset
4 <token name="@TOOL_VERSION@">1.0.2</token>
3c9ad4adf8d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 9c9689f095805b738f654eed152900339753f6fd
iuc
parents: 0
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
0
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
6 </macros>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
7 <requirements>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">parse_mito_blast</requirement>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
9 </requirements>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
11 parse_mito_blast.py
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
12 --blastout '$blastout'
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
13 ]]>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
14 </command>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
15 <inputs>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
16 <param argument="blastout" type="data" format="tabular" label="Tabular file generated by mito-blast"/>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
17 </inputs>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
18 <outputs>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
19 <data name="cov_report" format="tabular" from_work_dir="cov_report.tsv" label="${tool.name} on ${on_string}" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
20 <data name="mito_scaff_names" format="txt" from_work_dir="mito_scaff_names.txt" label="contaminant scaffolds on ${on_string}" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
21 </outputs>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
22 <tests>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
23 <test>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
24 <param name="blastout" value="test_input.tsv" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
25 <output name="cov_report" file="test_cov_report.tsv" ftype="tabular" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
26 <output name="mito_scaff_names" file="test_mito_scaff_names.txt" ftype="txt" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
27 </test>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
28 </tests>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
29 <help><![CDATA[
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
30
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
31 This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output \
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
32 all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
33 collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
34 account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
35 sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
36 (sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
37 identity to a mitochondrial subject sequence. To use, pass a format 6 blast output (--blastout) and the desired name of the report.
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
38
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
39 NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
40 and will be sensitive to this order.
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
41 ]]>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
42 </help>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
43 <citations>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
44 <citation type="bibtex">
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
45 @misc{Danecek_et_al,
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
46 Author={Danecek, P., Schiffels, S., Durbin, R.},
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
47 title={Multiallelic calling model in bcftools (-m)},
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
48 url = {http://samtools.github.io/bcftools/call-m.pdf},}
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
49 </citation>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
50 </citations>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
iuc
parents:
diff changeset
51 </tool>