# 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 @@
-
-
-
-
-
-