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