Mercurial > repos > simon-gladman > snippy
annotate snippy-core.xml @ 22:577b1b17a0ff draft default tip
Added snippy-core tool
| author | simon-gladman |
|---|---|
| date | Thu, 09 Jun 2016 09:44:50 -0400 |
| parents | ebd7a957ff4b |
| children |
| rev | line source |
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| 19 | 1 <tool id="snippy-core" name="snippy-core" version="0.2.0"> |
| 18 | 2 |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.0">snippy</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 | |
| 20 | 10 <command interpreter="perl"> |
| 11 <![CDATA[ | |
| 18 | 12 |
| 13 snippy_core_wrapper.pl | |
| 14 $is_reference | |
| 15 --mincov $mincov | |
| 16 --indirs '${" ".join(map(str, $indirs))}' | |
| 17 | |
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18 ]]></command> |
| 18 | 19 |
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20 <inputs> |
| 21 | 21 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" /> |
| 18 | 22 <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." /> |
| 22 | 23 <param name="mincov" type="integer" value="10" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" /> |
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24 </inputs> |
| 18 | 25 |
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26 <outputs> |
| 18 | 27 <data format="fasta" name="alignment_fasta" label="${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" /> | |
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30 </outputs> |
| 18 | 31 |
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32 <help><![CDATA[ |
| 18 | 33 Synopsis: |
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34 Combine multiple Snippy folders into a core SNP alignment |
| 18 | 35 |
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36 Usage: |
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37 ../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ... |
| 18 | 38 |
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39 Options: |
| 18 | 40 |
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41 --help! This help. |
| 18 | 42 |
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43 --quiet! No output to stderr (default '0'). |
| 18 | 44 |
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45 --verbose! Verbose output (default '0'). |
| 18 | 46 |
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47 --inprefix=s Preferred input prefix of Snippy files (default 'snps'). |
| 18 | 48 |
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49 --prefix=s Output file prefix (default 'core'). |
| 18 | 50 |
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51 --noref! Exclude reference (default '0'). |
| 18 | 52 |
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53 --mincov=i Minimum depth of coverage to consider core (default '10'). |
| 18 | 54 |
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55 --aformat=s Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta'). |
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56 |
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57 ]]></help> |
| 18 | 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> |