Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.xml @ 12:7a418148319d draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Tue, 16 Feb 2021 07:08:25 +0000
parents 84a1a3f70407
children 02bf6425fc25
comparison
equal deleted inserted replaced
11:84a1a3f70407 12:7a418148319d
18 --thresh '$thresh' 18 --thresh '$thresh'
19 --phred '$phred' 19 --phred '$phred'
20 --trim '$trim' 20 --trim '$trim'
21 $chimera_correction 21 $chimera_correction
22 --outputFile '$output_xlsx' 22 --outputFile '$output_xlsx'
23 --outputFile2 '$output_xlsx2'
24 --outputFile3 '$output_xlsx3'
23 ]]> 25 ]]>
24 </command> 26 </command>
25 <inputs> 27 <inputs>
26 <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."/> 28 <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."/>
27 <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/> 29 <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/>
31 <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/> 33 <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/>
32 <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/> 34 <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/>
33 <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/> 35 <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/>
34 </inputs> 36 </inputs>
35 <outputs> 37 <outputs>
36 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/> 38 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
39 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
40 <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
37 </outputs> 41 </outputs>
38 <tests> 42 <tests>
39 <test> 43 <test>
40 <param name="file1" value="FreeBayes_test.vcf"/> 44 <param name="file1" value="FreeBayes_test.vcf"/>
41 <param name="file2" value="Interesting_Reads_test.trim.bam"/> 45 <param name="file2" value="Interesting_Reads_test.trim.bam"/>
43 <param name="file4" value="SSCS_counts_test.json"/> 47 <param name="file4" value="SSCS_counts_test.json"/>
44 <param name="thresh" value="0"/> 48 <param name="thresh" value="0"/>
45 <param name="phred" value="20"/> 49 <param name="phred" value="20"/>
46 <param name="trim" value="10"/> 50 <param name="trim" value="10"/>
47 <param name="chimera_correction" value="True"/> 51 <param name="chimera_correction" value="True"/>
48 <output name="output_xlsx" file="Variant_Analyzer_test.xlsx" decompress="true" lines_diff="2"/> 52 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
53 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
54 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
49 </test> 55 </test>
50 </tests> 56 </tests>
51 <help> <![CDATA[ 57 <help> <![CDATA[
52 **What it does** 58 **What it does**
53 59
72 stats of tags that carry a mutation in the SSCS at the same position a mutation 78 stats of tags that carry a mutation in the SSCS at the same position a mutation
73 is called in the DCS. 79 is called in the DCS.
74 80
75 **Output** 81 **Output**
76 82
77 The output is an XLSX file containing frequencies stats for DCS mutations based 83 The output are three XLSX files containing frequencies stats for DCS mutations based
78 on information from the raw reads. In addition to that a tier based 84 on information from the raw reads. In addition to that a tier based
79 classification is provided based on the amout of support for a true variant call. 85 classification is provided based on the amout of support for a true variant call.
80 86
81 ]]> 87 ]]>
82 </help> 88 </help>