# HG changeset patch # User iuc # Date 1494342959 14400 # Node ID 22a1a2406fe9297a25a6e52d136f8cdded50da3d # Parent bce4bd511f2941562a7f38b2573805515b2449fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 diff -r bce4bd511f29 -r 22a1a2406fe9 macros.xml --- a/macros.xml Fri Dec 18 19:46:20 2015 -0500 +++ b/macros.xml Tue May 09 11:15:59 2017 -0400 @@ -1,16 +1,17 @@ - samtools + samtools + 1.3.1 @misc{SAM_def, title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + url = {https://samtools.github.io/hts-specs/},} 10.1093/bioinformatics/btp352 10.1093/bioinformatics/btr076 @@ -41,7 +42,7 @@ - echo $(samtools --version | head -n 1)", "$(samtools --version | grep -o -E "htslib.*?") + &1 | grep Version]]> @@ -64,7 +65,5 @@ 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - - diff -r bce4bd511f29 -r 22a1a2406fe9 samtools_slice_bam.xml --- a/samtools_slice_bam.xml Fri Dec 18 19:46:20 2015 -0500 +++ b/samtools_slice_bam.xml Tue May 09 11:15:59 2017 -0400 @@ -1,43 +1,40 @@ - - BAM by genomic regions - - macros.xml - - - - - - - + BAM by genomic regions + + macros.xml + + + + + + + - + samtools sort + -O bam + -T sorted + -@ \${GALAXY_SLOTS:-1} + -o '${output_bam}' + unsorted_output.bam + ]]> - + @@ -45,7 +42,7 @@ - + @@ -75,49 +72,43 @@ - - - - + - + - - + + - + - + - + - + - - UCSC Main**. +Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. +BED datasets can be obtained from **Get Data -> UCSC Main**. This tool is based on ``samtools view`` command. @no-chrom-options@ - -]]> - - + ]]> + diff -r bce4bd511f29 -r 22a1a2406fe9 tool_dependencies.xml --- a/tool_dependencies.xml Fri Dec 18 19:46:20 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -