Mercurial > repos > iuc > lumpy_prep
changeset 1:80adce82354c draft default tip
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit 41cb10683d89fa20e122f4c60b8f5bf0e3c390d8"
| author | iuc |
|---|---|
| date | Sat, 10 Jul 2021 07:40:25 +0000 |
| parents | 21f2361c32c9 |
| children | |
| files | lumpy_preprocessing.xml macros.xml |
| diffstat | 2 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/lumpy_preprocessing.xml Thu Nov 12 16:48:34 2020 +0000 +++ b/lumpy_preprocessing.xml Sat Jul 10 07:40:25 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@"> +<tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@" profile="20.05"> <description>extracts discordant read pairs and split-read alignments from a BAM dataset</description> <macros> <import>macros.xml</import> @@ -7,6 +7,8 @@ <requirement type="package" version="@TOOL_VERSION@">lumpy-sv</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ +set -o pipefail; + samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam && samtools view -b -F 1294 blasted.bam > discordants.unsorted.bam && @@ -34,9 +36,9 @@ <test> <param name="bam_in" ftype="bam" value="sample.bam" /> <param name="dup_handling" value="" /> - <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" /> - <output name="discordants_bam" ftype="bam" file="discordants.bam" /> - <output name="splitters_bam" ftype="bam" file="splitters.bam" /> + <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" lines_diff="2"/> + <output name="discordants_bam" ftype="bam" file="discordants.bam" lines_diff="2"/> + <output name="splitters_bam" ftype="bam" file="splitters.bam" lines_diff="2"/> </test> </tests> <help><![CDATA[
--- a/macros.xml Thu Nov 12 16:48:34 2020 +0000 +++ b/macros.xml Sat Jul 10 07:40:25 2021 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token> <token name="@TOOL_VERSION@">0.3.1</token> <xml name="citations"> <citations>