# HG changeset patch
# User brenninc
# Date 1463048451 14400
# Node ID a993f4a9aeaaab8adb9ddb5b7dd3fd6689335f20
Uploaded
diff -r 000000000000 -r a993f4a9aeaa bedToBam.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedToBam.xml Thu May 12 06:20:51 2016 -0400
@@ -0,0 +1,52 @@
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+ converter
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+ macros.xml
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+ samtools
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+ unsorted.bam &&
+ samtools sort -@ \${GALAXY_SLOTS:-1} -o '$output' -O bam -T dataset 'unsorted.bam'
+]]>
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diff -r 000000000000 -r a993f4a9aeaa macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu May 12 06:20:51 2016 -0400
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+ bedtools
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+ 2.24
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+ bedtools --version
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+ #set $col = list()
+ #set $op = list()
+ #for $item in $c_and_o_argument_repeat:
+ #silent $col.append( str($item.col) )
+ #silent $op.append( str($item.operation) )
+ #end for
+ #if $col:
+ -c #echo ','.join($col)#
+ -o #echo ','.join($op)#
+ #end if
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+`_
+]]>
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+ 10.1093/bioinformatics/btq033
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diff -r 000000000000 -r a993f4a9aeaa test-data/bedToBam1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedToBam1.bed Thu May 12 06:20:51 2016 -0400
@@ -0,0 +1,5 @@
+chr1 100 200 foo
+chr1 180 250 bar
+chr1 250 500 world
+chr1 501 1000 peace
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diff -r 000000000000 -r a993f4a9aeaa test-data/bedToBam_result.bam
Binary file test-data/bedToBam_result.bam has changed
diff -r 000000000000 -r a993f4a9aeaa test-data/mm9_chr1.len
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_chr1.len Thu May 12 06:20:51 2016 -0400
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+chr1 197195432
diff -r 000000000000 -r a993f4a9aeaa test-data/sortedBedToBam_result.bam
Binary file test-data/sortedBedToBam_result.bam has changed
diff -r 000000000000 -r a993f4a9aeaa tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu May 12 06:20:51 2016 -0400
@@ -0,0 +1,9 @@
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