Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.xml @ 16:30aec05d04d3 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Mon, 22 Feb 2021 14:33:12 +0000 |
parents | 6f4c61123a36 |
children | f06067bedfc5 |
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15:6f4c61123a36 | 16:30aec05d04d3 |
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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' | |
26 ]]> | 27 ]]> |
27 </command> | 28 </command> |
28 <inputs> | 29 <inputs> |
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."/> | 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."/> |
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."/> | 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."/> |
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."/> | 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."/> |
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."/> | 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."/> |
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."/> | 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."/> |
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."/> | 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."/> |
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."/> | 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."/> |
37 <param name="delim_csv" type="string" label="Delimiter in csv file" value="," help="Delimiter in csv summary file. Default = comma."/> | 38 <param name="delim_csv" type="text" label="Delimiter in csv file" value="," help="Delimiter in csv summary file. Default = comma."/> |
38 </inputs> | 39 </inputs> |
39 <outputs> | 40 <outputs> |
40 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> | 41 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> |
41 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> | 42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> |
42 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> | 43 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> |