Mercurial > repos > mheinzl > variant_analyzer2
diff mut2sscs.xml @ 72:3691922baa08 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Fri, 19 Mar 2021 14:05:39 +0000 |
| parents | d21960b45a6b |
| children | 6ccff403db8a |
line wrap: on
line diff
--- a/mut2sscs.xml Fri Mar 19 13:54:14 2021 +0000 +++ b/mut2sscs.xml Fri Mar 19 14:05:39 2021 +0000 @@ -1,15 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.1" profile="19.01"> +<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.1.0" profile="19.01"> <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description> <macros> <import>va_macros.xml</import> </macros> - <requirements> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.4.0">matplotlib</requirement> - <requirement type="package" version="0.15">pysam</requirement> - <requirement type="package" version="0.11.6">cyvcf2</requirement> - </requirements> + <expand macro="requirements"/> <command><![CDATA[ ln -s '$file2' bam_input.bam && ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && @@ -43,7 +38,7 @@ **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 single stranded consensus sequence (SSCS) reads. This file can be obtained by the tool `Map with BWA-MEM