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comparison read2mut.xml @ 42:da224c392a54 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 Wed, 24 Feb 2021 14:20:17 +0000
parents afda74e874ac
children d21960b45a6b
comparison
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41:db3ed9202516 42:da224c392a54
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="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="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"/>
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="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."/> 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."/>
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="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="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at the beginning of reads to lower tier. Default 10."/> 36 <param name="trim5" type="integer" label="Trimming threshold at 5' end of reads" value="10" help="Integer threshold for assigning mutations at the beginning of reads to a 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 the end of reads to lower tier. Default 10."/> 37 <param name="trim3" type="integer" label="Trimming threshold at 3' end of reads" value="10" help="Integer threshold for assigning mutations at the end of reads to a 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 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."/>
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <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 ${on_string}: XLSX summary"/>
42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> 42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
51 <param name="file4" value="SSCS_counts_test.json"/> 51 <param name="file4" value="SSCS_counts_test.json"/>
52 <param name="thresh" value="0"/> 52 <param name="thresh" value="0"/>
53 <param name="phred" value="20"/> 53 <param name="phred" value="20"/>
54 <param name="trim5" value="10"/> 54 <param name="trim5" value="10"/>
55 <param name="trim3" value="10"/> 55 <param name="trim3" value="10"/>
56 <param name="delim_csv" value=","/>
57 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> 56 <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"/> 57 <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"/> 58 <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"/> 59 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
61 </test> 60 </test>
69 from the raw reads. 68 from the raw reads.
70 69
71 **Input** 70 **Input**
72 71
73 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 72 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
74 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. 73 generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.
75 74
76 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the 75 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the
77 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. 76 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
78 77
79 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool 78 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool
85 is called in the DCS. 84 is called in the DCS.
86 85
87 **Output** 86 **Output**
88 87
89 The output are three XLSX files containing frequencies stats for DCS mutations based 88 The output are three XLSX files containing frequencies stats for DCS mutations based
90 on information from the raw reads. In addition to that a tier based 89 on information from the raw reads and a CSV file containing the summary information without color-coding. In addition to that a tier based
91 classification is provided based on the amout of support for a true variant call. 90 classification is provided based on the amout of support for a true variant call.
92 91
93 ]]> 92 ]]>
94 </help> 93 </help>
95 <expand macro="citation" /> 94 <expand macro="citation" />