# HG changeset patch
# User iuc
# Date 1673444471 0
# Node ID 20ad2e231693121f5e21ed550ab949a0032ecfef
# Parent 9dbf707bebb0323cd1f0e91d8d65944fdbeabeda
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split.xml
--- a/bamtools_split.xml Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
-
- BAM datasets on variety of attributes
-
- macros.xml
-
-
-
- $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
- ]]>
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-**What is does**
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-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
-
-
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- 10.1093/bioinformatics/btr174
-
-
diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split_mapped.xml
--- a/bamtools_split_mapped.xml Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
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- macros.xml
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-**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
-
-
-**How it works**
-
-Splits the input BAM file into 2 output files named (MAPPED) and (UNMAPPED) containing mapped and unmapped reads, respectively.
-
------
-
-.. class:: infomark
-
-**More information**
-
-Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
-
-
-
- 10.1093/bioinformatics/btr174
-
-
diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split_paired.xml
--- a/bamtools_split_paired.xml Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
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- macros.xml
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-**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
-
-
-**How it works**
-
-
-Splits the input BAM file into 2 output files named (SINGLE_END) and (PAIRED_END) containing single_end and paired_end reads, respectively.
-
------
-
-.. class:: infomark
-
-**More information**
-
-Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
-
-
-
- 10.1093/bioinformatics/btr174
-
-
diff -r 9dbf707bebb0 -r 20ad2e231693 bamtools_split_tag.xml
--- a/bamtools_split_tag.xml Wed Jan 11 12:03:53 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-
- into dataset list collection
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- macros.xml
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-
-
-**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 tag value can produce very large numbers of outputs. Read below and know what you are doing.
-
------
-
-**How it works**
-
-Split alignments by tag name into a dataset list collection.
-
-This can generate a huge number of output datasets depending on the number of distinct values of the TAG.
-
-
------
-
-.. class:: infomark
-
-**More information**
-
-Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
-
-
-
- 10.1093/bioinformatics/btr174
-
-