Mercurial > repos > greg > cfsan_snp_pipeline_call_sites

comparison cfsan_snp_pipeline_call_sites.xml @ 1:9ab66ea409ff draft

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author greg
date Tue, 21 Nov 2023 22:08:55 +0000
parents 02ab4f93ebd0
children 991fbae39ee6
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0:02ab4f93ebd0 1:9ab66ea409ff
13 <inputs> 13 <inputs>
14 <param name="input" label="Read alignment to reference" type="data" format="bam"/> 14 <param name="input" label="Read alignment to reference" type="data" format="bam"/>
15 <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/> 15 <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/>
16 </inputs> 16 </inputs>
17 <outputs> 17 <outputs>
18 <data name="calls" label="${input.name.split(' ')[0]} unfiltered SNPs" format="vcf"/> 18 <data name="calls" label="Call Sites (unfiltered SNPs)" format="vcf"/>
19 <data name="pileup" label="${input.name.split(' ')[0]} pileup" format="pileup"/> 19 <data name="pileup" label="Call Sites (pileup)" format="pileup"/>
20 <data name="metrics" label="Metrics from Picard" format="txt"/> 20 <data name="metrics" label="Call sites (Picard metrics)" format="txt"/>
21 <data label="S3 Cache log" name="cache_log" format="txt"/>
22 </outputs> 21 </outputs>
23 <tests> 22 <tests>
24 <test> 23 <test>
25 <param name="reference" value="lambda_virus.fasta"/> 24 <param name="reference" value="lambda_virus.fasta"/>
26 <param name="input" value="reads.bam"/> 25 <param name="input" value="reads.bam"/>
27 <output name="calls" ftype="vcf"> 26 <output name="calls" ftype="vcf">
28 <assert_contents> 27 <assert_contents>
29 <has_size value="9976" delta="100"/> 28 <has_size value="9976" delta="100"/>
30 </assert_contents> 29 </assert_contents>
31 </output> 30 </output>
32 <output name="pileup" ftype="pileup"> 31 <output name="pileup" ftype="pileup">
33 <assert_contents> 32 <assert_contents>
34 <has_size value="4259620" delta="100"/> 33 <has_size value="4259620" delta="100"/>
35 </assert_contents> 34 </assert_contents>
36 </output> 35 </output>
37 </test> 36 </test>
38 </tests> 37 </tests>
39 <help><![CDATA[ 38 <help><![CDATA[
40 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> 39 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>