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annotate mut2sscs.xml @ 9:5800e3acb06d draft

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author mheinzl
date Thu, 04 Feb 2021 08:57:57 +0000
parents 11a2a34f8a2b
children 84a1a3f70407
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1 <?xml version="1.0" encoding="UTF-8"?>
6
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2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.0" profile="19.01">
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3 <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description>
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4 <macros>
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5 <import>va_macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="2.7">python</requirement>
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9 <requirement type="package" version="1.4.0">matplotlib</requirement>
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10 <requirement type="package" version="0.15">pysam</requirement>
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11 <requirement type="package" version="0.11.6">cyvcf2</requirement>
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12 </requirements>
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13 <command><![CDATA[
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14 ln -s '$file2' bam_input.bam &&
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
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16 python '$__tool_directory__/mut2sscs.py'
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17 --mutFile '$file1'
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18 --bamFile bam_input.bam
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19 --outputJson '$output_json'
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
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24 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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25 </inputs>
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26 <outputs>
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27 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="file1" value="FreeBayes_test.vcf"/>
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32 <param name="file2" value="SSCS_test.bam"/>
11a2a34f8a2b planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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33 <output name="output_json" file="SSCS_counts_test.json" lines_diff="2"/>
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34 </test>
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35 </tests>
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36 <help> <![CDATA[
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37 **What it does**
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38
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39 Takes a VCF file with DCS mutations and a BAM file of aligned SSCS reads
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40 as input and writes statistics about tags of reads that carry a mutation in the
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41 SSCS at the same position a mutation is called in the DCS to a user specified output file..
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43 **Input**
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44
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45 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
11a2a34f8a2b planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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46 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
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48 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS)
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49 reads. This file can be obtained by the tool `Map with BWA-MEM
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50 <https://arxiv.org/abs/1303.3997>`_.
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52 **Output**
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53
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54 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS
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55 at the same position a mutation is called in the DCS.
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56
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57 ]]>
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58 </help>
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59 <expand macro="citation" />
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60 </tool>