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annotate mut2sscs.xml @ 0:5441e79a30f2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
author iuc
date Wed, 20 Nov 2019 22:47:11 +0000
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children 833d9e71b864
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5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.0" 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 </requirements>
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12 <command><![CDATA[
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13 ln -s '$file2' bam_input.bam &&
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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14 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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15 python '$__tool_directory__/mut2sscs.py'
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16 --mutFile '$file1'
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17 --bamFile bam_input.bam
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18 --outputJson '$output_json'
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
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23 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
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24 </inputs>
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25 <outputs>
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26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
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31 <param name="file2" value="SSCS_test_data_VA.bam"/>
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32 <output name="output_json" file="SSCS_counts_test_data_VA.json" lines_diff="2"/>
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33 </test>
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34 </tests>
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35 <help> <![CDATA[
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36 **What it does**
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37
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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38 Takes a tabular file with DCS mutations and a BAM file of aligned SSCS reads
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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39 as input and writes statistics about tags of reads that carry a mutation in the
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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40 SSCS at the same position a mutation is called in the DCS to a user specified output file..
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41
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42 **Input**
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43
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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44 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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45 generated by the **Variant Annotator** tool.
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46
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47 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS)
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48 reads. This file can be obtained by the tool `Map with BWA-MEM
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49 <https://arxiv.org/abs/1303.3997>`_.
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50
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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51 **Dataset 3:** Tabular file with reads as produced by the
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52 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
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53 <https://doi.org/10.1186/s13059-016-1039-4>`_
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54
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55 **Output**
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56
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57 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS
5441e79a30f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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58 at the same position a mutation is called in the DCS.
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59
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60 ]]>
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61 </help>
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62 <expand macro="citation" />
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63 </tool>