| Next changeset 1:45f0ce0a9f63 (2023-01-11) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a" |
|
added:
bamtools_split_tag.xml macros.xml test-data/bamtools-input-paired.bam test-data/bamtools-input-tags.bam test-data/bamtools-input1.bam test-data/bamtools-input2.bam test-data/bamtools-split-test1.bam test-data/bamtools_input2.chr1 test-data/bamtools_input_tags.TAG_XG_N.bam test-data/bamtools_input_tags.TAG_XG_V.bam test-data/split_bam.MAPPED.bam test-data/split_bam.PAIRED_END.bam test-data/split_bam.SINGLE_END.bam test-data/split_bam.UNMAPPED.bam |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 bamtools_split_tag.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools_split_tag.xml Sat Nov 27 10:02:45 2021 +0000 |
| [ |
| @@ -0,0 +1,71 @@ +<tool id="bamtools_split_tag" name="Split BAM by Tag" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>into dataset list collection</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + <![CDATA[ + #import re + #set $name = 'split_bam' + $re.sub('\W','_',$re.sub('\.bam$','',$input_bam.name)) + ln -s '${input_bam}' 'localbam.bam' && + ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' && + bamtools split -tag $tag_name + -in 'localbam.bam' + -stub '$name' + ]]> + </command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM dataset to split by tag value"/> + <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> + </inputs> + <outputs> + <collection name="output_bams" type="list" label="${input_bam.name} Split List"> + <discover_datasets pattern="split_bam(?P<designation>.+)\.bam" ext="bam" visible="false"/> + </collection> + </outputs> + <tests> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input-tags.bam"/> + <param name="tag_name" value="XG"/> + <output_collection name="output_bams" type="list"> + <element name="bamtools_input_tags.TAG_XG_V" file="bamtools_input_tags.TAG_XG_V.bam" compare="sim_size" delta="500" /> + </output_collection> + </test> + + </tests> + <help> +**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 + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Nov 27 10:02:45 2021 +0000 |
| b |
| @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">2.5.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bamtools</requirement> + <requirement type="package" version="1.4.1">samtools</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools-input-paired.bam |
| b |
| Binary file test-data/bamtools-input-paired.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools-input-tags.bam |
| b |
| Binary file test-data/bamtools-input-tags.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools-input1.bam |
| b |
| Binary file test-data/bamtools-input1.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools-input2.bam |
| b |
| Binary file test-data/bamtools-input2.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools-split-test1.bam |
| b |
| Binary file test-data/bamtools-split-test1.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools_input2.chr1 |
| b |
| Binary file test-data/bamtools_input2.chr1 has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools_input_tags.TAG_XG_N.bam |
| b |
| Binary file test-data/bamtools_input_tags.TAG_XG_N.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/bamtools_input_tags.TAG_XG_V.bam |
| b |
| Binary file test-data/bamtools_input_tags.TAG_XG_V.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/split_bam.MAPPED.bam |
| b |
| Binary file test-data/split_bam.MAPPED.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/split_bam.PAIRED_END.bam |
| b |
| Binary file test-data/split_bam.PAIRED_END.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/split_bam.SINGLE_END.bam |
| b |
| Binary file test-data/split_bam.SINGLE_END.bam has changed |
| b |
| diff -r 000000000000 -r c9fbbe6f5fc8 test-data/split_bam.UNMAPPED.bam |
| b |
| Binary file test-data/split_bam.UNMAPPED.bam has changed |