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1 <tool id="rtg_snp" name="Call SNPs">
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2 <description>from SAM files with rtg snp</description>
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3 <command interpreter="bash">galaxy-rtg-singleoutput-wrapper.sh $output $output.id $__new_file_path__ snps.vcf
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4 snp -t ${template.extra_files_path}
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5 --max-as-mated $maxscore
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6 --max-as-unmated $maxuscore
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7 --machine-errors $machine
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8 $input1
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9 #for $i in $inputs
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10 ${i.input}
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11 #end for
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12 -Z
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13 </command>
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14 <inputs>
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15 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
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16 <param name="maxscore" type="integer" value="3" label="Maximum alignment score for mated reads"/>
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17 <param name="maxuscore" type="integer" value="1" label="Maximum alignment score for umated reads"/>
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18 <param name="machine" type="select" label="Select machine type">
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19 <option value="illumina">Illumina</option>
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20 <option value="cg">Complete Genomics</option>
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21 <option value="454_se">454 single-end</option>
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22 <option value="454_pe">454 paired-end</option>
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23 </param>
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24 <param name="input1" label="First tabix-ed SAM file" type="data" format="samix" />
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25 <repeat name="inputs" title="Input tabix-ed SAM Files">
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26 <param name="input" label="Add file" type="data" format="samix" />
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27 </repeat>
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28 </inputs>
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29 <outputs>
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30 <data name="output" format="vcf" />
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31 </outputs>
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32
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33 <help>
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34 This tool calls snps from SAM files
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35 </help>
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36
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37 </tool>
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