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phe_samtools_mpileup.xml |
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| diff -r 65b5406977c9 -r 5b63d9a21d01 phe_samtools_mpileup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phe_samtools_mpileup.xml Mon Dec 21 07:24:59 2015 -0500 |
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| @@ -0,0 +1,32 @@ +<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> |