Mercurial > repos > artbio > repenrich2
diff repenrich2.xml @ 6:388a47ca4199 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit a9af1284d644055565b6cf3401569694218ab8e9
| author | artbio |
|---|---|
| date | Mon, 22 Apr 2024 10:31:50 +0000 |
| parents | 08e50af788f7 |
| children |
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--- a/repenrich2.xml Sun Apr 21 21:52:40 2024 +0000 +++ b/repenrich2.xml Mon Apr 22 10:31:50 2024 +0000 @@ -38,16 +38,16 @@ bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} input.fastq | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b -q 38 aligned.bam -o unique.bam && - samtools view -@ "\${GALAXY_SLOTS:-4}" -h -F 4 -b aligned.bam \ - | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ - | bedtools bamtofastq -i /dev/stdin -fq multimap.fastq && + samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b aligned.bam + | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null && + bedtools bamtofastq -i filt_aligned.bam -fq multimap.fastq && #else: bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} -1 input.fastq -2 input_2.fastq | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b -q 38 aligned.bam -o unique.bam && - samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam \ - | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -n - - + samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam + | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null && + samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -n filt_aligned.bam | bedtools bamtofastq -i /dev/stdin -fq multimap_1.fastq -fq2 multimap_2.fastq && #end if samtools index unique.bam &&