Mercurial > repos > mvdbeek > samblaster
diff samblaster.xml @ 2:5d1a1388a036 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
| author | mvdbeek |
|---|---|
| date | Sun, 18 Dec 2016 07:54:53 -0500 |
| parents | 4f68e55100c3 |
| children |
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--- a/samblaster.xml Fri Dec 16 05:44:40 2016 -0500 +++ b/samblaster.xml Sun Dec 18 07:54:53 2016 -0500 @@ -1,11 +1,16 @@ -<tool id="samblaster" name="samblaster" version="0.1.24.1"> +<tool id="samblaster" name="samblaster" version="0.1.24.2"> <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description> <requirements> <requirement type="package" version="0.1.24">samblaster</requirement> - <requirement type="package" version="1.3.1">samtools</requirement> + <requirement type="package" version="0.6.5">sambamba</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - samtools sort -@ \$GALAXY_SLOTS:-4 -m 4G -O sam -n '$input' | + #if $input.is_of_type('sam'): + #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input + #else: + #set stream="'%s'" % $input + #end if + sambamba view -t \${GALAXY_SLOTS:-4} -h <(sambamba sort -t \${GALAXY_SLOTS:-4} -n $stream -o /dev/stdout) | samblaster $output $discordantFile @@ -20,13 +25,22 @@ --maxUnmappedBases '$maxUnmappedBases' --minIndelSize '$minIndelSize' --minNonOverlap '$minNonOverlap' - --minClipSize '$minClipSize' && sleep 1 + --minClipSize '$minClipSize' + #if $output != "-o /dev/null": + && sambamba sort -o output.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam output.sam) + #end if + #if $discordantFile: + && sambamba sort -o discordant.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam discordant.sam) + #end if + #if $splitterFile: + && sambamba sort -o splitter.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam splitter.sam) + #end if ]]></command> <inputs> <param name="input" argument="--input" type="data" format="bam,sam"/> - <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o output.bam)" falsevalue="-o /dev/null"/> - <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o discordant.bam)" falsevalue=""/> - <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o splitter.bam)" falsevalue=""/> + <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o output.sam" falsevalue="-o /dev/null"/> + <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d discordant.sam" falsevalue=""/> + <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s splitter.sam" falsevalue=""/> <param name="unmappedFile" argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/> <param name="acceptDupMarks" argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/> <param name="excludeDups" argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/> @@ -60,8 +74,18 @@ <param name="discordandFile" value="false"/> <param name="splitterFile" value="true"/> <param name="unmappedFile" value="true"/> - <output name="output_bam" file="output.bam"/> - <output name="splitter_bam" file="splitters.bam"/> + <output name="output_bam" file="output.bam" lines_diff="10"/> + <output name="splitter_bam" file="splitters.bam" lines_diff="10"/> + <output name="unmapped_fastq" file="unmapped.fastq"/> + </test> + <test> + <param name="input" value="sr.input.sam" ftype="sam"/> + <param name="output" value="true"/> + <param name="discordandFile" value="false"/> + <param name="splitterFile" value="true"/> + <param name="unmappedFile" value="true"/> + <output name="output_bam" file="output.bam" lines_diff="10"/> + <output name="splitter_bam" file="splitters.bam" lines_diff="10"/> <output name="unmapped_fastq" file="unmapped.fastq"/> </test> </tests>