# HG changeset patch # User iuc # Date 1494342982 14400 # Node ID 2311187710fbfcc6b8bbd2df21e42fa3d450b1c5 # Parent ee06ec9cf0a6dc0135343df76db278cc09322730 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 diff -r ee06ec9cf0a6 -r 2311187710fb macros.xml --- a/macros.xml Fri Dec 18 19:45:25 2015 -0500 +++ b/macros.xml Tue May 09 11:16:22 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 ee06ec9cf0a6 -r 2311187710fb samtools_phase.xml --- a/samtools_phase.xml Fri Dec 18 19:45:25 2015 -0500 +++ b/samtools_phase.xml Tue May 09 11:16:22 2017 -0400 @@ -1,12 +1,13 @@ - + heterozygous SNPs - macros.xml - - - - - samtools phase -b "phase_wrapper" + macros.xml + + + + + + '$input_bam' > '$phase_sets' + ]]> @@ -28,12 +32,12 @@ - - - - - - + + + + + + @@ -81,50 +85,10 @@ - + - +Call and phase heterozygous SNPs. + ]]> + diff -r ee06ec9cf0a6 -r 2311187710fb tool_dependencies.xml --- a/tool_dependencies.xml Fri Dec 18 19:45:25 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -