Mercurial > repos > dave > dynamic_downsample
changeset 0:20823bce09e7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/downsample commit dd00e60bdbb1fb45d395bb59dd60795e39867624
| author | dave |
|---|---|
| date | Tue, 24 Sep 2019 16:20:27 -0400 |
| parents | |
| children | 03aeb837e398 |
| files | downsample.xml |
| diffstat | 1 files changed, 33 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/downsample.xml Tue Sep 24 16:20:27 2019 -0400 @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<tool id="dynamic_downsample" name="Dynamically downsample" version="1.0.0"> + <description>reads to desired coverage</description> + <requirements> + <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="5.0.1">gawk</requirement> + </requirements> + <command><![CDATA[ + if FACTOR=\$(samtools depth '$reads' | awk '{ a[i++]=\$3; } END { x=int((i+1)/2); if (x < (i+1)/2) y=(a[x-1]+a[x])/2; else y=a[x-1]; f = 1/(y/$coverage) ; if (f >= 1) exit 1 ; else print f }') ; + then samtools view '$reads' -s \$FACTOR -O $reads.datatype -o '$output' ; + else ; + cp '$reads' '$output' + fi + ]]> + </command> + <inputs> + <param name="reads" type="data" format="sam,bam" label="Reads to downsample" /> + <param name="coverage" type="integer" value="1000" label="Target coverage" /> + </inputs> + <outputs> + <data format="bam" name="output" label="${tool.name} on ${on_string} (Downsampled to ${coverage}x coverage)"> + <change_format> + <when input="reads" value="sam" format="sam" /> + </change_format> + </data> + </outputs> + <tests> + </tests> + <help> + </help> + <citations> + </citations> +</tool>