Mercurial > repos > jjohnson > bamtools_split_ref
changeset 0:a83b275f7c41 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Mon, 19 Jun 2017 12:56:32 -0400 |
| parents | |
| children | |
| files | ._bamtools_split_ref.xml bamtools_split_ref.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 |
| diffstat | 14 files changed, 88 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools_split_ref.xml Mon Jun 19 12:56:32 2017 -0400 @@ -0,0 +1,88 @@ +<tool id="bamtools_split_ref" name="Split BAM by Reference" version="2.4.0"> + <description>into dataset list collection</description> + <requirements> + <requirement type="package" version="2.4.0">bamtools</requirement> + </requirements> + <command> + <![CDATA[ + ln -s '${input_bam}' 'localbam.bam' && + ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' && + bamtools split -reference + -in localbam.bam + -stub split_bam + ## Preserve order from metadata in the output collection + #import re + #set $name = $re.sub('\W','_',$re.sub('\.bam$','',$input_bam.name)) + #if str($refs) != 'None': + #set $ref_list = ' '.join(str($refs).split(",")) + #else + #set $ref_list = ' '.join([$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')]) + #end if + && mkdir -p outputs + && (export I=0; + for i in $ref_list; + do I=\$((++I)); SN=`printf "split_bam.REF_%s.bam" "\$i"`; + if [ -e \$SN ]; then FN=`printf "outputs/split_bam%05d%s.%s.bam" \$((I)) '$name' "\$i"`; mv \$SN \$FN; fi; + done) + ]]> + </command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM dataset to split by reference"/> + <param name="refs" type="select" optional="True" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" > + <help><![CDATA[Click and type in the box above to see options. You can select multiple entries. + If "No options available" is displayed, you need to re-detect metadata on the input dataset. + ]]></help> + <options> + <filter type="data_meta" ref="input_bam" key="reference_names" /> + </options> + </param> + </inputs> + <outputs> + <collection name="output_bams" type="list" label="${input_bam.name} Split List"> + <discover_datasets pattern="split_bam\d*(?P<designation>.+)\.bam" ext="bam" directory="outputs" visible="false"/> + </collection> + </outputs> + <tests> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input2.bam"/> + <output_collection name="output_bams" type="list"> + <element name="bamtools_input2.chr1" file="bamtools_input2.chr1" 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 reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing. + +----- + +**How it works** + +Split alignments by reference name into a dataset list collection. The collection will be in the same order as the input BAM references. + +In cases of unfinished genomes with very large number of reference sequences (scaffolds) +it can generate thousands (if not millions) of output datasets. + + +----- + +.. 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>