Mercurial > repos > bgruening > sambamba_merge
changeset 0:305a4f796bd3 draft default tip
planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
| author | bgruening |
|---|---|
| date | Mon, 10 Feb 2025 19:11:44 +0000 |
| parents | |
| children | |
| files | Sambamba_merge.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.txt 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 | 13 files changed, 74 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Sambamba_merge.xml Mon Feb 10 19:11:44 2025 +0000 @@ -0,0 +1,44 @@ +<tool id="sambamba_merge" name="Sambamba merge" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> + <description>Merge several BAM files into one</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ + sambamba merge + -l $compression_level + '${output}' + #for $infile in $input_bam: + '${infile}' + #end for + --nthreads \${GALAXY_SLOTS:-8} + ]]></command> + <inputs> + <param name="input_bam" type="data" format="qname_sorted.bam,bam" multiple="true" label="Input BAM files to be merged" help="Please note that the sorting order of all input files must be the same"/> + <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"/> + </inputs> + <outputs> + <data name="output" format_source="input_files"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_bam" value="qname_sorted.bam,qname_sorted.bam"/> + <param name="compression_level" value="5"/> + <output name="output" file="qname_sorted_merged.bam" lines_diff="4"/> + </test> + <test expect_num_outputs="1"> + <param name="input_bam" value="coordinate_sorted.bam,coordinate_sorted.bam"/> + <param name="compression_level" value="5"/> + <output name="output" file="coordinate_sorted_merged.bam" lines_diff="4"/> + </test> + </tests> + <help> +<![CDATA[ + +sambamba_merge is used to merge several sorted BAM files into one. The sorting order of all the files must be the same, and it is maintained in the output file. + +SAM headers are merged automatically like in Picard merging tool. +]]> + </help> + <expand macro="citations" /> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 10 19:11:44 2025 +0000 @@ -0,0 +1,17 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.1</token> + <token name="@SUFFIX_VERSION@">2</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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.markdup.txt Mon Feb 10 19:11:44 2025 +0000 @@ -0,0 +1,13 @@ + +sambamba 1.0.1 + by Artem Tarasov and Pjotr Prins (C) 2012-2023 + LDC 1.39.0 / DMD v2.109.1 / LLVM17.0.6 / bootstrap LDC - the LLVM D compiler (1.39.0) + +finding positions of the duplicate reads in the file... + sorted 0 end pairs + and 4 single ends (among them 0 unmatched pairs) + collecting indices of duplicate reads... done in 0 ms + found 3 duplicates +collected list of positions in 0 min 0 sec +marking duplicates... +collected list of positions in 0 min 0 sec