Mercurial > repos > iuc > ivar_consensus
comparison ivar_consensus.xml @ 11:3e4f434a69c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
| author | iuc |
|---|---|
| date | Wed, 11 Jan 2023 09:53:52 +0000 |
| parents | f362150bef41 |
| children | 9c5754002592 |
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| 10:e319b5b65879 | 11:3e4f434a69c6 |
|---|---|
| 1 <tool id="ivar_consensus" name="ivar consensus" version="@VERSION@+galaxy0"> | 1 <tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
| 2 <description>Call consensus from aligned BAM file</description> | 2 <description>Call consensus from aligned BAM file</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements"/> |
| 7 <expand macro="version_command" /> | 7 <expand macro="version_command"/> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 #import re | 9 #import re |
| 10 #set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier)) | 10 #set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier)) |
| 11 ln -s '$input_bam' sorted.bam && | 11 ln -s '$input_bam' sorted.bam && |
| 12 samtools mpileup -A -d 0 -Q 0 sorted.bam | ivar consensus | 12 samtools mpileup -A -d 0 -Q 0 sorted.bam | ivar consensus |