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author | ulfschaefer |
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date | Mon, 21 Dec 2015 07:24:59 -0500 |
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children | 0af0acbd73f7 |
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<tool id="phe_samtools_mpileup" name="PHE MPileup" version="1.0"> <description>PHE SNP and indel caller</description> <requirements> <requirement type="package" version="1.1">samtools</requirement> </requirements> <command interpreter="bash"> phe_samtools_mpileup.sh $input_bam $ref_file $outvcf </command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM file" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </inputs> <outputs> <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" /> </outputs> <tests> <test> <param name="input_bam" value="in_short.bam" ftype="bam" /> <param name="ref_file" value="ref.fa" ftype="fasta" /> <output name="outvcf" file="out.vcf" ftype="vcf" /> </test> </tests> <help> **Citation** For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> </tool>