Mercurial > repos > simon-gladman > snippy
comparison snippy-core.xml @ 6:15f5a3074012 draft
Added snippy core and static binaries for linux and mac.
| author | simon-gladman |
|---|---|
| date | Thu, 09 Jun 2016 20:15:42 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 5:ff31f16f5dfd | 6:15f5a3074012 |
|---|---|
| 1 <tool id="snippy-core" name="snippy-core" version="0.2.0"> | |
| 2 | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.0">snippy</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 | |
| 10 <command interpreter="perl"> | |
| 11 <![CDATA[ | |
| 12 | |
| 13 snippy_core_wrapper.pl | |
| 14 $is_reference | |
| 15 --mincov $mincov | |
| 16 --indirs '${" ".join(map(str, $indirs))}' | |
| 17 | |
| 18 ]]></command> | |
| 19 | |
| 20 <inputs> | |
| 21 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" /> | |
| 22 <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." /> | |
| 23 <param name="mincov" type="integer" value="10" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" /> | |
| 24 </inputs> | |
| 25 | |
| 26 <outputs> | |
| 27 <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln" /> | |
| 28 <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab" /> | |
| 29 <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt" /> | |
| 30 </outputs> | |
| 31 | |
| 32 <help><![CDATA[ | |
| 33 Synopsis: | |
| 34 Combine multiple Snippy folders into a core SNP alignment | |
| 35 | |
| 36 Usage: | |
| 37 ../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ... | |
| 38 | |
| 39 Options: | |
| 40 | |
| 41 --help! This help. | |
| 42 | |
| 43 --quiet! No output to stderr (default '0'). | |
| 44 | |
| 45 --verbose! Verbose output (default '0'). | |
| 46 | |
| 47 --inprefix=s Preferred input prefix of Snippy files (default 'snps'). | |
| 48 | |
| 49 --prefix=s Output file prefix (default 'core'). | |
| 50 | |
| 51 --noref! Exclude reference (default '0'). | |
| 52 | |
| 53 --mincov=i Minimum depth of coverage to consider core (default '10'). | |
| 54 | |
| 55 --aformat=s Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta'). | |
| 56 | |
| 57 ]]></help> | |
| 58 | |
| 59 <citations> | |
| 60 <citation type="bibtex">@UNPUBLISHED{Seemann2013, | |
| 61 author = "Seemann T", | |
| 62 title = "snippy: fast bacterial variant calling from NGS reads", | |
| 63 year = "2015", | |
| 64 note = "https://github.com/tseemann/snippy"}</citation> | |
| 65 </citations> | |
| 66 | |
| 67 </tool> |