Mercurial > repos > bgruening > sambamba_sort
changeset 0:87c1b543c4c4 draft default tip
planemo upload for repository https://github.com/biod/sambamba commit 13ed0b409cf2c5de007e0a6fa93391cbbb21795d
| author | bgruening |
|---|---|
| date | Wed, 12 Jun 2024 15:01:40 +0000 |
| parents | |
| children | |
| files | Sambamba_sort.xml macros.xml test-data/1.bam test-data/1.coord.sorted.bam test-data/1.qname.sorted.bam test-data/2.bam test-data/2.markdup.bam test-data/2.markdup_removed.bam test-data/coordinate_sorted.bam test-data/coordinate_sorted_merged.bam test-data/qname_sorted.bam test-data/qname_sorted_merged.bam |
| diffstat | 12 files changed, 80 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Sambamba_sort.xml Wed Jun 12 15:01:40 2024 +0000 @@ -0,0 +1,63 @@ +<tool id="sambamba_sort" name="Sambamba sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> + <description>Tool to sort BAM files</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + sambamba sort + -o '${output}' + $sort_order + #if $filter + -F '${filter}' + #end if + -l $compression_level + '${input_bam}' + --tmpdir '\${TMPDIR:-.}' + --nthreads \${GALAXY_SLOTS:-4} + ]]></command> + <inputs> + <param name="input_bam" type="data" format="qname_input_sorted.bam,qname_sorted.bam,bam" label="Input BAM file"/> + <param name="sort_order" type="select" label="Select sorting mode"> + <option value="" selected="true">Coordinate based</option> + <option value="-n">Sort by read name lexicographically</option> + </param> + <param argument="--compression-level" type="integer" value="5" min="0" max="9" label="Level of compression for merged BAM file, number from 0 to 9"/> + <param argument="--filter" type="text" optional="true" label="Keep only reads that satisfy this filter" help="You could select reads spanning a targeted region, by using the following filter: chr6:1000-5000"/> + </inputs> + <outputs> + <data name="output" format="bam"> + <change_format> + <when input="sort_order" value="-n" format="qname_sorted.bam"/> + </change_format> + </data> + </outputs> + <tests> + <!--Test case of QNAME sorted BAM file--> + <test expect_num_outputs="1"> + <param name="input_bam" value="1.bam" ftype="bam"/> + <param name="compression_level" value="5"/> + <param name="sort_order" value="-n"/> + <output name="output" file="1.qname.sorted.bam" ftype="qname_sorted.bam" lines_diff="4"/> + </test> + <!--Test case of Coordinate sorted BAM file--> + <test expect_num_outputs="1"> + <param name="input_bam" value="1.bam" ftype="bam"/> + <param name="compression_level" value="5"/> + <param name="sort_order" value=""/> + <output name="output" file="1.coord.sorted.bam" ftype="bam" lines_diff="4"/> + </test> + </tests> + <help> +<![CDATA[ + +Sambamba sort performs sorting of BAM files. + +BAM files can have either 'coordinate' or 'qname' sort order. + - 'coordinate' sorting order : Sorts Reads by (integer) reference ID, and for each reference sort corresponding reads by start coordinate. + - 'qname' sorting order : Reads are sorted lexicographically by their names. + +]]> + </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jun 12 15:01:40 2024 +0000 @@ -0,0 +1,17 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.1</token> + <token name="@SUFFIX_VERSION@">1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.0.1">sambamba</requirement> + <yield/> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btv098</citation> + <yield /> + </citations> + </xml> +</macros>