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1 <tool id="call_sites" name="CFSAN SNP pipeline: call sites" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>of high-confidence SNPs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 cp '$reference' 'reference.fasta' &&
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9 samtools faidx 'reference.fasta' &&
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10 samtools view -b -F 4 '$input' -o ./unsorted.bam &&
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11 samtools sort -o ./sorted.bam -O BAM ./unsorted.bam &&
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12 picard MarkDuplicates INPUT=./sorted.bam OUTPUT=/dev/stdout METRICS_FILE='$metrics' | samtools mpileup -f ./reference.fasta - -o '$pileup' &&
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13 varscan mpileup2snp '$pileup' --min_var-freq 0.90 --output-vcf 1 > '$calls'
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14 ]]></command>
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15 <inputs>
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16 <param name="input" label="Read alignment to reference" type="data" format="sam"/>
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17 <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/>
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18 </inputs>
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19 <outputs>
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20 <data name="calls" label="Call Sites (unfiltered SNPs)" format="vcf"/>
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21 <data name="pileup" label="Call Sites (pileup)" format="pileup"/>
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22 <data name="metrics" label="Call sites (Picard metrics)" format="txt"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="reference" value="lambda_virus.fasta"/>
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27 <param name="input" value="reads.sam"/>
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28 <output name="calls" ftype="vcf">
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29 <assert_contents>
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30 <has_size value="9976" delta="100"/>
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1
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31 </assert_contents>
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32 </output>
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33 <output name="pileup" ftype="pileup">
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34 <assert_contents>
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35 <has_size value="4259620" delta="100"/>
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36 </assert_contents>
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37 </output>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 **What it does**
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42
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43 Finds the sites with high-confidence SNPs in a sample.
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44
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45 **More information**
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46
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47 CFSAN SNP Pipeline `call consensus documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#call-consensus>`_
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48 ]]></help>
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49 <expand macro="citations"/>
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50 </tool>
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51
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