Mercurial > repos > iuc > ivar_variants

annotate ivar_variants.xml @ 0:12d66d0d05ac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
author iuc
date Mon, 30 Mar 2020 07:45:57 -0400
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children 147465efa99c
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12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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1 <tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy0">
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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2 <description>Call variants from aligned BAM file</description>
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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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 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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9 ln -s '$ref' ref.fa &&
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10 ln -s '$input_bam' sorted.bam &&
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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11 samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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12 -p variants
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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13 -q $min_qual
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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14 -t $min_freq
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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15 ]]> </command>
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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16 <inputs>
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17 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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18 <param name="ref" type="data" format="fasta" label="Reference"/>
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19 <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/>
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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20 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/>
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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21 </inputs>
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22 <outputs>
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23 <data name="output_variants" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="variants.tsv"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" />
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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28 <param name="ref" value="zika/db/PRV.fa" />
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29 <output name="output_variants" file="zika/Z52_a.tsv" lines_diff="10"/>
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 iVar uses the output of the samtools mpileup command to call variants -
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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34 single nucleotide variants(SNVs) and indels. In order to call variants
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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35 correctly, the reference file used for alignment must be passed to iVar
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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36 using the -r flag. The output of samtools pileup is piped into ivar variants
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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37 to generate a .tsv file with the variants. There are two parameters that can
12d66d0d05ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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38 be set for variant calling using iVar - minimum quality(Default: 20) and
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39 minimum frequency(Default: 0.03). Minimum quality is the minimum quality for
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40 a base to be counted towards the ungapped depth to canculate iSNV frequency
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41 at a given position. For insertions, the quality metric is discarded and the
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42 mpileup depth is used directly. Minimum frequency is the minimum frequency
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43 required for a SNV or indel to be reported.
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44
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45 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
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46 ]]> </help>
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47 <expand macro="citations" />
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48 </tool>