Mercurial > repos > mheinzl > variant_analyzer2
changeset 42:da224c392a54 draft
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 | db3ed9202516 |
children | d21960b45a6b |
files | read2mut.py read2mut.xml |
diffstat | 2 files changed, 6 insertions(+), 7 deletions(-) [+] |
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--- a/read2mut.py Wed Feb 24 13:14:28 2021 +0000 +++ b/read2mut.py Wed Feb 24 14:20:17 2021 +0000 @@ -60,9 +60,9 @@ parser.add_argument('--phred', type=int, default=20, help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.') parser.add_argument('--trim5', type=int, default=10, - help='Integer threshold for assigning mutations at start of reads to lower tier. Default 10.') + help='Integer threshold for assigning mutations at the beginning of the reads to lower tier. Default 10.') parser.add_argument('--trim3', type=int, default=10, - help='Integer threshold for assigning mutations at end of reads to lower tier. Default 10.') + help='Integer threshold for assigning mutations at the end of the reads to lower tier. Default 10.') parser.add_argument('--chimera_correction', action="store_true", help='Count chimeric variants and correct the variant frequencies') return parser
--- a/read2mut.xml Wed Feb 24 13:14:28 2021 +0000 +++ b/read2mut.xml Wed Feb 24 14:20:17 2021 +0000 @@ -33,8 +33,8 @@ <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."/> <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."/> <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."/> - <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."/> - <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."/> + <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."/> + <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."/> <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."/> </inputs> <outputs> @@ -53,7 +53,6 @@ <param name="phred" value="20"/> <param name="trim5" value="10"/> <param name="trim3" value="10"/> - <param name="delim_csv" value=","/> <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/> <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/> <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/> @@ -71,7 +70,7 @@ **Input** **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. -generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. +generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller. **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. @@ -87,7 +86,7 @@ **Output** The output are three XLSX files containing frequencies stats for DCS mutations based -on information from the raw reads. In addition to that a tier based +on information from the raw reads and a CSV file containing the summary information without color-coding. In addition to that a tier based classification is provided based on the amout of support for a true variant call. ]]>