Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.xml @ 19:858ca8b7ad43 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 15:02:21 +0000 |
parents | f06067bedfc5 |
children | cf6f0fb05bad |
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18:d910b6dfd826 | 19:858ca8b7ad43 |
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1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.0.3" profile="17.01"> | 2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.0.4" profile="17.01"> |
3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> | 3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> |
4 <macros> | 4 <macros> |
5 <import>va_macros.xml</import> | 5 <import>va_macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"> | 7 <expand macro="requirements"> |
15 --bamFile bam_input.bam | 15 --bamFile bam_input.bam |
16 --inputJson '$file3' | 16 --inputJson '$file3' |
17 --sscsJson '$file4' | 17 --sscsJson '$file4' |
18 --thresh '$thresh' | 18 --thresh '$thresh' |
19 --phred '$phred' | 19 --phred '$phred' |
20 --trim '$trim' | 20 --trim5 '$trim5' |
21 --trim3 '$trim3' | |
21 $chimera_correction | 22 $chimera_correction |
22 --outputFile '$output_xlsx' | 23 --outputFile '$output_xlsx' |
23 --outputFile_csv '$outputFile_csv' | 24 --outputFile_csv '$outputFile_csv' |
24 --outputFile2 '$output_xlsx2' | 25 --outputFile2 '$output_xlsx2' |
25 --outputFile3 '$output_xlsx3' | 26 --outputFile3 '$output_xlsx3' |
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."/> |
31 <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/> | 32 <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/> |
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="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at start of reads to lower tier. Default 10."/> |
37 <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at 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."/> | 38 <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 </inputs> | 39 </inputs> |
38 <outputs> | 40 <outputs> |
39 <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 ${on_string}: XLSX summary"/> |
40 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> | 42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> |
47 <param name="file2" value="Interesting_Reads_test.trim.bam"/> | 49 <param name="file2" value="Interesting_Reads_test.trim.bam"/> |
48 <param name="file3" value="tag_count_dict_test.json"/> | 50 <param name="file3" value="tag_count_dict_test.json"/> |
49 <param name="file4" value="SSCS_counts_test.json"/> | 51 <param name="file4" value="SSCS_counts_test.json"/> |
50 <param name="thresh" value="0"/> | 52 <param name="thresh" value="0"/> |
51 <param name="phred" value="20"/> | 53 <param name="phred" value="20"/> |
52 <param name="trim" value="10"/> | 54 <param name="trim5" value="10"/> |
55 <param name="trim3" value="10"/> | |
53 <param name="delim_csv" value=","/> | 56 <param name="delim_csv" value=","/> |
54 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> | 57 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> |
55 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/> | 58 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/> |
56 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> | 59 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> |
57 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> | 60 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/> |