Mercurial > repos > iuc > bamtools_split_ref
changeset 2:20ad2e231693 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
| author | iuc |
|---|---|
| date | Wed, 11 Jan 2023 13:41:11 +0000 |
| parents | 9dbf707bebb0 |
| children | 9b520009db81 |
| files | bamtools_split.xml bamtools_split_mapped.xml bamtools_split_paired.xml bamtools_split_tag.xml |
| diffstat | 4 files changed, 0 insertions(+), 303 deletions(-) [+] |
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--- 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 @@ -<tool id="bamtools_split" name="Split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>BAM datasets on variety of attributes</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="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"/> - <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>
--- 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 @@ -<tool id="bamtools_split_mapped" name="Split BAM by Mapped" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description></description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <command> - <![CDATA[ - ln -s '${input_bam}' 'localbam.bam' && - ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' && - bamtools split -mapped - -in localbam.bam - -stub split_bam - ]]> - </command> - <inputs> - <param name="input_bam" type="data" format="bam" label="BAM dataset to split by mapped/unmapped"/> - </inputs> - <outputs> - <data format="bam" name="mapped" label="${input_bam.name} mapped" from_work_dir="split_bam.MAPPED.bam" /> - <data format="bam" name="unmapped" label="${input_bam.name} unmapped" from_work_dir="split_bam.UNMAPPED.bam" /> - </outputs> - <tests> - <test> - <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> - <output name="mapped" file="split_bam.MAPPED.bam" compare="sim_size" delta="200" /> - <output name="unmapped" file="split_bam.UNMAPPED.bam" compare="sim_size" delta="200" /> - </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 - - -**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 - - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btr174</citation> - </citations> -</tool>
--- 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 @@ -<tool id="bamtools_split_paired" name="Split BAM by Paired/Single End" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description></description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <command> - <![CDATA[ - ln -s '${input_bam}' 'localbam.bam' && - ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' && - bamtools split -paired - -in localbam.bam - -stub split_bam - ]]> - </command> - <inputs> - <param name="input_bam" type="data" format="bam" label="BAM dataset to split by single_end/paired_end"/> - </inputs> - <outputs> - <data format="bam" name="single" label="${input_bam.name} mapped" from_work_dir="split_bam.SINGLE_END.bam" /> - <data format="bam" name="paired" label="${input_bam.name} unmapped" from_work_dir="split_bam.PAIRED_END.bam" /> - </outputs> - <tests> - <test> - <param name="input_bam" ftype="bam" value="bamtools-input-paired.bam"/> - <output name="single" file="split_bam.SINGLE_END.bam" compare="sim_size" delta="200" /> - <output name="paired" file="split_bam.PAIRED_END.bam" compare="sim_size" delta="200" /> - </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 - - -**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 - - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btr174</citation> - </citations> -</tool>
--- 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 @@ -<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>