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comparison 5_call_consensus.xml @ 50:e90a783a4e8b

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Thu, 09 May 2019 11:45:22 -0400
parents ebfa7fd256aa
children d53281e6edae
comparison
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49:ebfa7fd256aa 50:e90a783a4e8b
1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10"> 1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
2 <description>for a sample, or lookup cached consensus SNP calls</description> 2 <description>for a sample, or lookup cached consensus SNP calls</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.6">bzip2</requirement> 4 <requirement type="package" version="1.0.6">bzip2</requirement>
5 <requirement type="package" version="1.0.1">snp-pipeline</requirement> 5 <requirement type="package" version="2.0.2">snp-pipeline</requirement>
6 <requirement type="package" version="1.9.134">boto3</requirement> 6 <requirement type="package" version="1.9.134">boto3</requirement>
7 <requirement type="package" version="3.7.3">python</requirement> 7 <requirement type="package" version="3.6.8">python</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
11 #set $identifier = $call_pileup.name.split(' ')[0] 11 #set $identifier = $call_pileup.name.split(' ')[0]
12 python3 $__tool_directory__/snp-cache.py snp_consenus_calls 12 python $__tool_directory__/snp-cache.py snp_consenus_calls
13 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 13 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
14 -c " 14 -c "
15 mkdir ./$identifier/ 15 mkdir -p ./$identifier/
16 && cp $call_pileup ./$identifier/reads.all.pileup 16 && cp $call_pileup ./$identifier/reads.all.pileup
17 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta 17 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta
18 " 18 "
19 -l $cache_log 19 -l $cache_log
20 | tar zvx ./ 20 | tar zvx ./
35 <tests> 35 <tests>
36 <test> 36 <test>
37 <param name="snps" value="snplist.txt" /> 37 <param name="snps" value="snplist.txt" />
38 <param name="calls" value="samples/sample1/var.flt.vcf" /> 38 <param name="calls" value="samples/sample1/var.flt.vcf" />
39 <param name="call_pileup" value="samples/sample1/reads.all.pileup" /> 39 <param name="call_pileup" value="samples/sample1/reads.all.pileup" />
40 <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="6" /> 40 <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="20" />
41 <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" /> 41 <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" />
42 </test> 42 </test>
43 </tests> 43 </tests>
44 <help><![CDATA[ 44 <help><![CDATA[
45 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> 45 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>