Mercurial > repos > ulfschaefer > phe_samtools_mpileup
comparison phe_samtools_mpileup.xml @ 4:5b63d9a21d01 draft
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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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3:65b5406977c9 | 4:5b63d9a21d01 |
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1 <tool id="phe_samtools_mpileup" name="PHE MPileup" version="1.0"> | |
2 <description>PHE SNP and indel caller</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.1">samtools</requirement> | |
5 </requirements> | |
6 <command interpreter="bash"> | |
7 phe_samtools_mpileup.sh $input_bam $ref_file $outvcf | |
8 </command> | |
9 <inputs> | |
10 <param name="input_bam" type="data" format="bam" label="BAM file" /> | |
11 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
12 </inputs> | |
13 <outputs> | |
14 <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" /> | |
15 </outputs> | |
16 <tests> | |
17 <test> | |
18 <param name="input_bam" value="in_short.bam" ftype="bam" /> | |
19 <param name="ref_file" value="ref.fa" ftype="fasta" /> | |
20 <output name="outvcf" file="out.vcf" ftype="vcf" /> | |
21 </test> | |
22 </tests> | |
23 <help> | |
24 | |
25 **Citation** | |
26 | |
27 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>`_ | |
28 | |
29 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* | |
30 | |
31 </help> | |
32 </tool> |