Mercurial > repos > iuc > samtools_markdup
changeset 5:887e02a45734 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
| author | iuc |
|---|---|
| date | Wed, 22 Jun 2022 07:48:23 +0000 |
| parents | 8c440c3002bc |
| children | b5527cc104ab |
| files | samtools_markdup.xml |
| diffstat | 1 files changed, 8 insertions(+), 2 deletions(-) [+] |
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--- a/samtools_markdup.xml Sun Dec 19 15:56:46 2021 +0000 +++ b/samtools_markdup.xml Wed Jun 22 07:48:23 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@" profile="@PROFILE@" > +<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" > <description>marks duplicate alignments</description> <macros> <import>macros.xml</import> @@ -19,6 +19,12 @@ ln -s '$bamfile' coordsort.sam && #end if +## copy fasta reference if needed +## because samtools will try to write a .fai file next to it +#if $output_options.output_format.select_oformat == "CRAM" + ln -s '$output_options.output_format.ref_file' ref_file.fa && +#end if + samtools markdup -@ \$addthreads @@ -39,7 +45,7 @@ #end if -O $output_options.output_format.select_oformat #if $output_options.output_format.select_oformat == "CRAM" - --reference '$output_options.output_format.ref_file' + --reference ref_file.fa #end if coordsort.sam '$output'