Mercurial > repos > devteam > bamtools_split
changeset 3:9676127a1ed2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
| author | iuc |
|---|---|
| date | Wed, 04 Dec 2019 07:47:03 -0500 |
| parents | e2c1b62e1db1 |
| children | 0a7b0989fa09 |
| files | bamtools-split.xml bamtools_split.xml macros.xml test-data/bamtools-input-paired.bam test-data/bamtools-input-tags.bam test-data/bamtools-input2.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 | 13 files changed, 134 insertions(+), 108 deletions(-) [+] |
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--- 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 @@ -<tool id="bamSplit" name="Split" version="2.4.0"> - <description>BAM datasets on variety of attributes</description> - <requirements> - <requirement type="package" version="2.4.0">bamtools</requirement> - </requirements> - <command> - <![CDATA[ - echo "BAM" > $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 - ]]> - </command> - <inputs> - <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> - <conditional name="analysis_type"> - <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option"> - <option value="-mapped">Mapping status (-mapped)</option> - <option value="-paired">Pairing status (-paired)</option> - <option value="-reference">Reference name (-reference)</option> - <option value="-tag">Specific tag (-tag)</option> - </param> - <when value="-mapped" /> - <when value="-paired" /> - <when value="-reference" /> - <when value="-tag"> - <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> - <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> - </data> - </outputs> - <tests> - <test> - <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> - <param name="analysis_type_selector" value="-mapped"/> - <output name="report"> - <assert_contents> - <has_line line="BAM" /> - </assert_contents> - <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> - </output> - </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** - -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 - - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btr174</citation> - </citations> -</tool>
--- /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 @@ +<tool id="bamtools_split" name="Split" version="2.4.0"> + <description>BAM datasets on variety of attributes</description> + <requirements> + <requirement type="package" version="2.4.0">bamtools</requirement> + </requirements> + <command> + <![CDATA[ + echo "BAM" > $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 + ]]> + </command> + <inputs> + <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> + <conditional name="analysis_type"> + <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option"> + <option value="-mapped">Mapping status (-mapped)</option> + <option value="-paired">Pairing status (-paired)</option> + <option value="-reference">Reference name (-reference)</option> + <option value="-tag">Specific tag (-tag)</option> + </param> + <when value="-mapped" /> + <when value="-paired" /> + <when value="-reference" /> + <when value="-tag"> + <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> + <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> + </data> + </outputs> + <tests> + <test> + <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> + <param name="analysis_type_selector" value="-mapped"/> + <output name="report"> + <assert_contents> + <has_line line="BAM" /> + </assert_contents> + <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> + </output> + </test> + <test> + <param name="input_bams" ftype="bam" value="bamtools-input2.bam"/> + <param name="analysis_type_selector" value="-reference"/> + <param name="output_type" value="dataset_collection"/> + <output name="report"> + <assert_contents> + <has_line line="BAM" /> + </assert_contents> + <discovered_dataset designation="REF_chr1" file="bamtools_input2.chr1" ftype="bam"/> + </output> + </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** + +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 + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> +</tool>
--- /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 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">2.4.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@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