annotate phe_samtools_mpileup.xml @ 1:59eca98715b4 draft

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author ulfschaefer
date Mon, 21 Dec 2015 07:22:34 -0500
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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 </requirements>
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6 <command interpreter="bash">
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7 phe_samtools_mpileup.sh $input_sam $ref_file $outvcf
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8 </command>
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9 <inputs>
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10 <param name="input_sam" type="data" format="sam" label="SAM file" />
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11 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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12 </inputs>
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13 <outputs>
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14 <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="in_sam" value="in_short.sam" ftype="sam" />
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19 <param name="ref_file" value="ref.fa" ftype="fasta" />
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20 <output name="outvcf" file="out.vcf" ftype="vcf" />
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21 </test>
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22 </tests>
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23 <help>
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24
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25 **Citation**
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26
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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
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28
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29 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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30
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31 </help>
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32 </tool>