Mercurial > repos > dfornika > artic_margin_cons_medaka

annotate artic_margin_cons_medaka.xml @ 1:9fcffca8f6ad draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
author dfornika
date Wed, 11 Mar 2020 02:00:01 +0000
parents 7df876ad836a
children 24c5caa214e7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
1 <tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0+galaxy0">
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
2 <description>Generate consensus fasta file from a reference fasta, bam alignment and VCF file</description>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
3 <requirements>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
4 <requirement type="package" version="0.6.8">pyvcf</requirement>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
5 <requirement type="package" version="1.76">biopython</requirement>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
6 </requirements>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
8 python '${__tool_directory__}/margin_cons_medaka.py'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
9 --depth '${minimum_depth}'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
10 --quality '${minimum_quality}'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
11 '${ref_fasta}'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
12 '${input_variants}'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
13 '${input_alignment}'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
14 > '${consensus_fasta}'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
15 2> '${report}'
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
16 ]]></command>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
17 <inputs>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
18 <param name="ref_fasta" type="data" format="fasta" label="Reference Sequence"/>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
19 <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
20 <param name="input_variants" type="data" format="vcf" label="Input Variants"/>
1
9fcffca8f6ad "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents: 0
diff changeset
21 <param name="minimum_depth" type="integer" value="5" min="1" max="500" label="Minimum depth to call a variant"/>
9fcffca8f6ad "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents: 0
diff changeset
22 <param name="minimum_quality" type="integer" value="0" min="0" max="100" label="Minimum quality to call a variant"/>
0
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
23 </inputs>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
24 <outputs>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
25 <data name="consensus_fasta" format="fasta" label="${tool.name} on ${on_string}: Consensus (.fasta)" />
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
26 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
27 </outputs>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
28 <tests>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
29 </tests>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
30 <help><![CDATA[
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
31 ]]></help>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
32 <citations>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
33 </citations>
7df876ad836a "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
dfornika
parents:
diff changeset
34 </tool>