# HG changeset patch
# User iuc
# Date 1575463623 18000
# Node ID 9676127a1ed278b920f0475a3460ef316e5f5897
# Parent e2c1b62e1db101c23b3452e673a9fc9665533153
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
diff -r e2c1b62e1db1 -r 9676127a1ed2 bamtools-split.xml
--- a/bamtools-split.xml Wed Jan 18 11:44:47 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-
- BAM datasets on variety of attributes
-
- bamtools
-
-
- $report &&
- #for $bam_count, $input_bam in enumerate( $input_bams ):
- ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
- ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
- #end for
- bamtools
- split
- #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
- ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
- #else
- ${analysis_type.analysis_type_selector}
- #end if
- -stub split_bam
- #for $bam_count, $input_bam in enumerate( $input_bams ):
- -in "localbam_${bam_count}.bam"
- #end for
- ]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**What is does**
-
-BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
-
------
-
-.. class:: warningmark
-
-**DANGER: Multiple Outputs**
-
-As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing.
-
------
-
-**How it works**
-
-The following options can be specified via "**Split BAM dataset(s) by**" dropdown::
-
- Mapping status (-mapped) split mapped/unmapped and generate two output files
- named (MAPPED) and (UNMAPPED) containing mapped and unmapped
- reads, respectively.
-
- Pairing status (-paired) split single-end/paired-end alignments and generate two output files
- named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
- reads, respectively.
-
- Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with
- very large number of reference sequences (scaffolds) it can generate
- thousands (if not millions) of output datasets.
-
- Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this
- option from the menu will allow you to enter the tag name. As was the
- case with the reference splitting above, this option can produce very
- large number of outputs if a tag has a large number of unique values.
-
------
-
-.. class:: infomark
-
-**More information**
-
-Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
-
-
-
- 10.1093/bioinformatics/btr174
-
-
diff -r e2c1b62e1db1 -r 9676127a1ed2 bamtools_split.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools_split.xml Wed Dec 04 07:47:03 2019 -0500
@@ -0,0 +1,119 @@
+
+ BAM datasets on variety of attributes
+
+ bamtools
+
+
+ $report &&
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
+ ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
+ #end for
+ bamtools
+ split
+ #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
+ ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
+ #else
+ ${analysis_type.analysis_type_selector}
+ #end if
+ -stub split_bam
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ -in "localbam_${bam_count}.bam"
+ #end for
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What is does**
+
+BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
+
+-----
+
+.. class:: warningmark
+
+**DANGER: Multiple Outputs**
+
+As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing.
+
+-----
+
+**How it works**
+
+The following options can be specified via "**Split BAM dataset(s) by**" dropdown::
+
+ Mapping status (-mapped) split mapped/unmapped and generate two output files
+ named (MAPPED) and (UNMAPPED) containing mapped and unmapped
+ reads, respectively.
+
+ Pairing status (-paired) split single-end/paired-end alignments and generate two output files
+ named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
+ reads, respectively.
+
+ Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with
+ very large number of reference sequences (scaffolds) it can generate
+ thousands (if not millions) of output datasets.
+
+ Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this
+ option from the menu will allow you to enter the tag name. As was the
+ case with the reference splitting above, this option can produce very
+ large number of outputs if a tag has a large number of unique values.
+
+-----
+
+.. class:: infomark
+
+**More information**
+
+Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
+
+
+
+ 10.1093/bioinformatics/btr174
+
+
diff -r e2c1b62e1db1 -r 9676127a1ed2 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Dec 04 07:47:03 2019 -0500
@@ -0,0 +1,15 @@
+
+
+ 2.4.0
+
+
+ bamtools
+ samtools
+
+
+
+
+ 10.1093/bioinformatics/btr174
+
+
+
\ No newline at end of file
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/bamtools-input-paired.bam
Binary file test-data/bamtools-input-paired.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/bamtools-input-tags.bam
Binary file test-data/bamtools-input-tags.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/bamtools-input2.bam
Binary file test-data/bamtools-input2.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/bamtools_input2.chr1
Binary file test-data/bamtools_input2.chr1 has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/bamtools_input_tags.TAG_XG_N.bam
Binary file test-data/bamtools_input_tags.TAG_XG_N.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/bamtools_input_tags.TAG_XG_V.bam
Binary file test-data/bamtools_input_tags.TAG_XG_V.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/split_bam.MAPPED.bam
Binary file test-data/split_bam.MAPPED.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/split_bam.PAIRED_END.bam
Binary file test-data/split_bam.PAIRED_END.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/split_bam.SINGLE_END.bam
Binary file test-data/split_bam.SINGLE_END.bam has changed
diff -r e2c1b62e1db1 -r 9676127a1ed2 test-data/split_bam.UNMAPPED.bam
Binary file test-data/split_bam.UNMAPPED.bam has changed