Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.xml @ 17:f06067bedfc5 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 Mon, 22 Feb 2021 14:40:07 +0000
parents 30aec05d04d3
children 858ca8b7ad43
comparison
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16:30aec05d04d3 17:f06067bedfc5
21 $chimera_correction 21 $chimera_correction
22 --outputFile '$output_xlsx' 22 --outputFile '$output_xlsx'
23 --outputFile_csv '$outputFile_csv' 23 --outputFile_csv '$outputFile_csv'
24 --outputFile2 '$output_xlsx2' 24 --outputFile2 '$output_xlsx2'
25 --outputFile3 '$output_xlsx3' 25 --outputFile3 '$output_xlsx3'
26 --delim_csv '$delim_csv'
27 ]]> 26 ]]>
28 </command> 27 </command>
29 <inputs> 28 <inputs>
30 <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."/> 29 <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."/>
31 <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."/> 30 <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."/>
33 <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/> 32 <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/>
34 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/> 33 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
35 <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."/> 34 <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."/>
36 <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."/> 35 <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."/>
37 <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."/> 36 <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."/>
38 <param name="delim_csv" type="text" label="Delimiter in csv file" value="," help="Delimiter in csv summary file. Default = comma."/>
39 </inputs> 37 </inputs>
40 <outputs> 38 <outputs>
41 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> 39 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> 40 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
43 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> 41 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
51 <param name="file4" value="SSCS_counts_test.json"/> 49 <param name="file4" value="SSCS_counts_test.json"/>
52 <param name="thresh" value="0"/> 50 <param name="thresh" value="0"/>
53 <param name="phred" value="20"/> 51 <param name="phred" value="20"/>
54 <param name="trim" value="10"/> 52 <param name="trim" value="10"/>
55 <param name="delim_csv" value=","/> 53 <param name="delim_csv" value=","/>
56 <param name="chimera_correction" value="True"/>
57 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> 54 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
58 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/> 55 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
59 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> 56 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
60 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> 57 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
61 </test> 58 </test>