# HG changeset patch # User iuc # Date 1494342975 14400 # Node ID 71d5c34fef4e69db736e5625e8aba3c28ed2e2a3 # Parent 4ab677d8c0de1049304cc0e6ec04b8a166460ccc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 diff -r 4ab677d8c0de -r 71d5c34fef4e macros.xml --- a/macros.xml Fri Dec 18 19:46:37 2015 -0500 +++ b/macros.xml Tue May 09 11:16:15 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 4ab677d8c0de -r 71d5c34fef4e samtools_sort.xml --- a/samtools_sort.xml Fri Dec 18 19:46:37 2015 -0500 +++ b/samtools_sort.xml Tue May 09 11:16:15 2017 -0400 @@ -1,12 +1,20 @@ - - BAM dataset + + order of storing aligned sequences - macros.xml - - - - - samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}" + macros.xml + + + + + @@ -29,12 +37,9 @@ - **What it does** This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. - - - + diff -r 4ab677d8c0de -r 71d5c34fef4e tool_dependencies.xml --- a/tool_dependencies.xml Fri Dec 18 19:46:37 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -