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comparison read2mut.xml @ 84:e46d5e377760 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
author mheinzl
date Fri, 19 Aug 2022 11:23:37 +0000
parents d7aea14291e8
children 97bd9c7a1b44
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83:8cec772c0bf1 84:e46d5e377760
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="3.0.0" profile="19.01"> 2 <tool id="read2mut" name="Call specific mutations in reads:" version="3.1.0" profile="19.01">
3 <description>Looks for reads with a mutation at known positions and calculates frequencies and stats.</description> 3 <description>Looks for reads with a 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">
17 --sscsJson '$file4' 17 --sscsJson '$file4'
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 $refalttiers
22 --softclipping_dist '$softclipping_dist' 23 --softclipping_dist '$softclipping_dist'
23 --reads_threshold '$reads_threshold' 24 --reads_threshold '$reads_threshold'
24 --outputFile '$output_xlsx' 25 --outputFile '$output_xlsx'
25 --outputFile_csv '$outputFile_csv' 26 --outputFile_csv '$outputFile_csv'
26 --outputFile2 '$output_xlsx2' 27 --outputFile2 '$output_xlsx2'
35 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occurring in DCS of less than thresh tags are displayed. Default of 0 displays all."/> 36 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occurring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
36 <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 is considered. Default = 20."/> 37 <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 is considered. Default = 20."/>
37 <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."/> 38 <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."/>
38 <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants (not for the reference allele) and correct the variant frequencies."/> 39 <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants (not for the reference allele) and correct the variant frequencies."/>
39 <param name="softclipping_dist" type="integer" label="Distance between artifact and softclipping of the reads" min="1" value="15" help="Count mutation as an artifact if mutation lies within this parameter away from the softclipping part of the reads. Default = 20"/> 40 <param name="softclipping_dist" type="integer" label="Distance between artifact and softclipping of the reads" min="1" value="15" help="Count mutation as an artifact if mutation lies within this parameter away from the softclipping part of the reads. Default = 20"/>
40 <param name="reads_threshold" type="float" label="Minimum percentage of softclipped reads in a family" min="0.0" max="1.0" value="1.0" help="Float number which specifies the minimum percentage of softclipped reads in a family to be considered in the softclipping tiers. Default: 1.0, means all reads of a family have to be softclipped."/> 41 <param name="reads_threshold" type="float" label="Minimum percentage of softclipped reads in a family" min="0.0" max="1.0" value="1.0" help="Float number which specifies the minimum percentage of softclipped reads in a family to be considered in the softclipping tiers. Default: 1.0, means all reads of a family have to be softclipped."/>
42 <param name="refalttiers" type="boolean" label="Extract tiers also for reference allele" truevalue="--refalttiers" falsevalue="" checked="False" help="Extracts tier information for the alternate and reference allele. Note that this will increase the running time of the tool. Otherwise only the tier information for the alternate allele is extracted."/>
41 </inputs> 43 </inputs>
42 <outputs> 44 <outputs>
43 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> 45 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
44 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> 46 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
45 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/> 47 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
55 <param name="phred" value="20"/> 57 <param name="phred" value="20"/>
56 <param name="trim" value="10"/> 58 <param name="trim" value="10"/>
57 <param name="chimera_correction"/> 59 <param name="chimera_correction"/>
58 <param name="softclipping_dist" value="15"/> 60 <param name="softclipping_dist" value="15"/>
59 <param name="reads_threshold" value="1.0"/> 61 <param name="reads_threshold" value="1.0"/>
62 <param name="refalttiers"/>
60 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true"/> 63 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true"/>
61 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true"/> 64 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true"/>
62 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true"/> 65 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true"/>
63 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true"/> 66 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true"/>
64 </test> 67 </test>
82 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool 85 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool
83 containing dictionaries of the tags of reads containing mutations 86 containing dictionaries of the tags of reads containing mutations
84 in the DCS. 87 in the DCS.
85 88
86 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool 89 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool
87 stats of tags that carry a mutation and the reference allele in the SSCS at the same position a mutation 90 stats of tags that carry a mutation (and optional the reference allele) in the SSCS at the same position a mutation
88 is called in the DCS. 91 is called in the DCS.
89 92
90 **Output** 93 **Output**
91 94
92 The output is three XLSX files containing frequencies stats for DCS mutations based 95 The output is three XLSX files containing frequencies stats for DCS mutations based