Mercurial > repos > simon-gladman > snippy

annotate snippy-core.xml @ 7:93d294cd4d59 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added snippy core
author simon-gladman
date Fri, 10 Jun 2016 00:10:22 -0400
parents 15f5a3074012
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
1 <tool id="snippy-core" name="snippy-core" version="0.2.0">
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
2
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
3 <requirements>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
4 <requirement type="package" version="3.0">snippy</requirement>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
5 </requirements>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
6 <stdio>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
7 <exit_code range="1:" />
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
8 </stdio>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
9
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
10 <command interpreter="perl">
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
11 <![CDATA[
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
12
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
13 snippy_core_wrapper.pl
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
14 $is_reference
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
15 --mincov $mincov
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
16 --indirs '${" ".join(map(str, $indirs))}'
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
17
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
18 ]]></command>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
19
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
20 <inputs>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
21 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
22 <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." />
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
23 <param name="mincov" type="integer" value="10" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" />
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
24 </inputs>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
25
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
26 <outputs>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
27 <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln" />
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
28 <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab" />
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
29 <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt" />
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
30 </outputs>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
31
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
32 <help><![CDATA[
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
33 Synopsis:
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
34 Combine multiple Snippy folders into a core SNP alignment
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
35
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
36 Usage:
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
37 ../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ...
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
38
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
39 Options:
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
40
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
41 --help! This help.
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
42
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
43 --quiet! No output to stderr (default '0').
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
44
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
45 --verbose! Verbose output (default '0').
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
46
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
47 --inprefix=s Preferred input prefix of Snippy files (default 'snps').
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
48
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
49 --prefix=s Output file prefix (default 'core').
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
50
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
51 --noref! Exclude reference (default '0').
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
52
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
53 --mincov=i Minimum depth of coverage to consider core (default '10').
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
54
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
55 --aformat=s Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta').
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
56
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
57 ]]></help>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
58
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
59 <citations>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
60 <citation type="bibtex">@UNPUBLISHED{Seemann2013,
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
61 author = "Seemann T",
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
62 title = "snippy: fast bacterial variant calling from NGS reads",
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
63 year = "2015",
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
64 note = "https://github.com/tseemann/snippy"}</citation>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
65 </citations>
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
66
15f5a3074012 Added snippy core and static binaries for linux and mac.
simon-gladman
parents:
diff changeset
67 </tool>