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annotate mut2sscs.xml @ 5:d9cbf833624e draft

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planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Tue, 27 Oct 2020 12:46:55 +0000
parents 9d74f30275c6
children 11a2a34f8a2b
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e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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1 <?xml version="1.0" encoding="UTF-8"?>
2
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2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.1" profile="19.01">
0
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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 <expand macro="requirements"/>
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8 <command><![CDATA[
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9 ln -s '$file2' bam_input.bam &&
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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11 python '$__tool_directory__/mut2sscs.py'
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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12 --mutFile '$file1'
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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13 --bamFile bam_input.bam
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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14 --outputJson '$output_json'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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19 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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20 </inputs>
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21 <outputs>
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22 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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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="file1" value="DCS_Mutations_test_data_VA.tabular"/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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27 <param name="file2" value="SSCS_test_data_VA.bam"/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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28 <output name="output_json" file="SSCS_counts_test_data_VA.json" lines_diff="2"/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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29 </test>
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30 </tests>
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31 <help> <![CDATA[
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32 **What it does**
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33
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34 Takes a tabular file with DCS mutations and a BAM file of aligned SSCS reads
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35 as input and writes statistics about tags of reads that carry a mutation in the
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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36 SSCS at the same position a mutation is called in the DCS to a user specified output file..
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38 **Input**
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39
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40 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as
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41 generated by the **Variant Annotator** tool.
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42
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43 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS)
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44 reads. This file can be obtained by the tool `Map with BWA-MEM
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45 <https://arxiv.org/abs/1303.3997>`_.
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46
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47 **Dataset 3:** Tabular file with reads as produced by the
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48 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
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49 <https://doi.org/10.1186/s13059-016-1039-4>`_
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50
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51 **Output**
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52
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53 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS
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54 at the same position a mutation is called in the DCS.
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55
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56 ]]>
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57 </help>
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58 <expand macro="citation" />
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59 </tool>