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1 <tool id="phe_samtools_mpileup" name="PHE MPileup" version="1.0">
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2 <description>PHE SNP and indel caller</description>
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3 <requirements>
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4 <requirement type="package" version="1.1">samtools</requirement>
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5 <requirement type="package" version="1.3">bcftools</requirement>
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6 </requirements>
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7 <stdio>
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8 <!-- Assume anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 </stdio>
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12 <command interpreter="bash">
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13 phe_samtools_mpileup.sh $input_bam $ref_file $outvcf
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14 </command>
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15 <inputs>
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16 <param name="input_bam" type="data" format="bam" label="BAM file" />
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17 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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18 </inputs>
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19 <outputs>
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20 <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input_bam" value="in_short.bam" ftype="bam" />
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25 <param name="ref_file" value="ref.fa" ftype="fasta" />
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26 <output name="outvcf" file="out.vcf" ftype="vcf" />
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27 </test>
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28 </tests>
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29 <help>
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30
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31 **Citation**
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32
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33 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>`_
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34
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35 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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36
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37 </help>
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38 </tool>
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