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annotate metasnp.xml @ 0:39dc67b8f847 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/metasnp commit 4d6ab8614d11d40412e9f904797a6a744d436146-dirty
author chrisd
date Thu, 14 Jul 2016 14:51:04 -0400
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children a3d1f2a85806
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39dc67b8f847 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/metasnp commit 4d6ab8614d11d40412e9f904797a6a744d436146-dirty
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1 <tool id="metasnp" name="MetaSNP" version="0.1.0">
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2 <description>A simple naive metagenomics variant caller</description>
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3 <requirements>
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4 <requirement type="package" version="0.1">meta_snp</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 <command><![CDATA[
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10 metasnp
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11 -amr_fp $reference
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12 #if $sam_type.mode == "single_end"
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13 -samse $sam_type.samse_input
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14 $sam_type.best
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15 #else
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16 -sampe $sam_type.sampe_input
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17 $sam_type.best
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18 #end if
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19 -out_fp $result
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20 ]]></command>
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21 <inputs>
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22 <param type="data" name="reference" format="fasta" label="Reference sequence"/>
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23 <conditional name="sam_type">
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24 <param name="mode" type="select" label="SAM file type">
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25 <option value="single_end"></option>
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26 <option value="paired_end"></option>
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27 </param>
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28 <when value="single_end">
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29 <param type="data" name="samse_input" format="sam" label="Single-end SAM file"/>
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30 <param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
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31 </when>
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32 <when value="paired_end">
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33 <param type="data" name="sampe_input" format="sam" label="Paired-end SAM file"/>
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34 <param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="result" format="tabular" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="mode" value="single_end"/>
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44 <param name="reference" value="ref.fa"/>
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45 <param name="samse_input" value="samse.sam"/>
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46 <output name="result" file="samse_result" ftype="tabular"/>
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47 </test>
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48 <test>
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49 <param name="mode" value="paired_end"/>
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50 <param name="reference" value="ref.fa"/>
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51 <param name="sampe_input" value="sampe.sam"/>
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52 <output name="result" file="sampe_result" ftype="tabular"/>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56 Program: metasnp
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57
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58 Usage: metasnp [options]
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59
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60 Options:
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61 -amr_fp amr database path
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62 -samse single-end sam file path
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63 -sampe paired-end sam file path
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64 -b filter on unique alignments
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65 ]]></help>
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66 <citations>
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67 </citations>
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68 </tool>