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comparison tools/rtg/snp.xml @ 1:8593828f91e7 default tip

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Full galaxy wrapper
author diego
date Sat, 21 Apr 2012 21:36:15 -0400
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0:d50638ebd809 1:8593828f91e7
1 <tool id="rtg_snp" name="Call SNPs">
2 <description>from SAM files with rtg snp</description>
3 <command interpreter="bash">galaxy-rtg-singleoutput-wrapper.sh $output $output.id $__new_file_path__ snps.vcf
4 snp -t ${template.extra_files_path}
5 --max-as-mated $maxscore
6 --max-as-unmated $maxuscore
7 --machine-errors $machine
8 $input1
9 #for $i in $inputs
10 ${i.input}
11 #end for
12 -Z
13 </command>
14 <inputs>
15 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
16 <param name="maxscore" type="integer" value="3" label="Maximum alignment score for mated reads"/>
17 <param name="maxuscore" type="integer" value="1" label="Maximum alignment score for umated reads"/>
18 <param name="machine" type="select" label="Select machine type">
19 <option value="illumina">Illumina</option>
20 <option value="cg">Complete Genomics</option>
21 <option value="454_se">454 single-end</option>
22 <option value="454_pe">454 paired-end</option>
23 </param>
24 <param name="input1" label="First tabix-ed SAM file" type="data" format="samix" />
25 <repeat name="inputs" title="Input tabix-ed SAM Files">
26 <param name="input" label="Add file" type="data" format="samix" />
27 </repeat>
28 </inputs>
29 <outputs>
30 <data name="output" format="vcf" />
31 </outputs>
32
33 <help>
34 This tool calls snps from SAM files
35 </help>
36
37 </tool>