# HG changeset patch
# User iuc
# Date 1632845692 0
# Node ID 8890e2d4c06862142cab81ad2dddee03a9d30a1f
# Parent 740ce0a18f0d3ed40299939055f946fe3bb34e35
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
diff -r 740ce0a18f0d -r 8890e2d4c068 macros.xml
--- a/macros.xml Sun Oct 14 13:44:49 2018 -0400
+++ b/macros.xml Tue Sep 28 16:14:52 2021 +0000
@@ -5,10 +5,16 @@
- 1.9
- #set $flags = sum(map(int, str($filter).split(',')))
+ 1.13
+ 20.05
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+merge multiple sorted alignment filesmacros.xml
@@ -8,36 +8,38 @@
&2 echo "inconsistently sorted input" &&
+ >&2 echo "inconsistently sorted input" &&
exit 1 &&
#end if
#end for
-
+#if $bed_file
+ #for $i, $bam in enumerate( $bamfiles ):
+ samtools index ${i}.sam &&
+ #end for
+#end if
samtools merge
-@ \$addthreads
-s $seed
## TODO force overwrite seems necessay (but I do not understand why ...)
--f
+-f
## Galaxy provides only default compression
## #if $compression == 'levelone'
## -1
@@ -51,13 +53,16 @@
-n
#end if
## TODO since galaxy can't represent this as data type at the moment this option is unsupported
-## -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
+## -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
#if str($region) != ''
-R '$region'
#end if
## Attach an RG tag to each alignment. The tag value is inferred from file names.
## -r
## TODO -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
+#if $bed_file:
+ -L '$bed_file'
+#end if
$idrg
$idpg
$output
@@ -67,6 +72,7 @@
]]>
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@@ -123,7 +136,7 @@
If a file to take @headers from is specified the @SQ headers of input files will be merged into the specified header, otherwise they will be merged into a composite header created from the input headers. If in the process of merging @SQ lines for coordinate sorted input files, a conflict arises as to the order (for example input1.bam has @SQ for a,b,c and input2.bam has b,a,c) then the resulting output file will need to be re-sorted back into coordinate order.
-Unless the @PG/@RG headers are made unique when merging @RG and @PG records into the output header then any IDs found to be duplicates of existing IDs in the output header will have a suffix appended to them to differentiate them from similar header records from other files and the read records will be updated to reflect this.
+Unless the @PG/@RG headers are made unique when merging @RG and @PG records into the output header then any IDs found to be duplicates of existing IDs in the output header will have a suffix appended to them to differentiate them from similar header records from other files and the read records will be updated to reflect this.
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/1.merge.expected.bam
Binary file test-data/1.merge.expected.bam has changed
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/2.merge.expected.bam
Binary file test-data/2.merge.expected.bam has changed
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/3.merge.expected.bam
Binary file test-data/3.merge.expected.bam has changed
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/4.merge.expected.bam
Binary file test-data/4.merge.expected.bam has changed
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/5.merge.expected.bam
Binary file test-data/5.merge.expected.bam has changed
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/6.merge.expected.bam
Binary file test-data/6.merge.expected.bam has changed
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/7.merge.expected.bam
Binary file test-data/7.merge.expected.bam has changed
diff -r 740ce0a18f0d -r 8890e2d4c068 test-data/test_input_1_a.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input_1_a.bed Tue Sep 28 16:14:52 2021 +0000
@@ -0,0 +1,14 @@
+insert 49 59 r000/1 30 +
+insert 79 89 r000/1/2 30 -
+ref1 6 22 r001/2 30 +
+ref1 8 18 r002 30 +
+ref1 8 14 r003 30 +
+ref1 15 40 r004 30 +
+ref1 28 33 r003 30 -
+ref1 36 45 r001/1 30 -
+ref2 0 20 x1 30 +
+ref2 1 22 x2 30 +
+ref2 5 27 x3 30 +
+ref2 9 34 x4 30 +
+ref2 11 35 x5 30 +
+ref2 13 36 x6 30 +