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comparison repenrich2.xml @ 6:388a47ca4199 draft

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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
comparison
equal deleted inserted replaced
5:08e50af788f7 6:388a47ca4199
36 36
37 #if $seq_method.seq_method_list == "single-read": 37 #if $seq_method.seq_method_list == "single-read":
38 bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} input.fastq 38 bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} input.fastq
39 | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && 39 | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 &&
40 samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b -q 38 aligned.bam -o unique.bam && 40 samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b -q 38 aligned.bam -o unique.bam &&
41 samtools view -@ "\${GALAXY_SLOTS:-4}" -h -F 4 -b aligned.bam \ 41 samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b aligned.bam
42 | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ 42 | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null &&
43 | bedtools bamtofastq -i /dev/stdin -fq multimap.fastq && 43 bedtools bamtofastq -i filt_aligned.bam -fq multimap.fastq &&
44 #else: 44 #else:
45 bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} -1 input.fastq -2 input_2.fastq 45 bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} -1 input.fastq -2 input_2.fastq
46 | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && 46 | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 &&
47 samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b -q 38 aligned.bam -o unique.bam && 47 samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b -q 38 aligned.bam -o unique.bam &&
48 samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam \ 48 samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam
49 | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ 49 | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null &&
50 | samtools sort -@ "\${GALAXY_SLOTS:-4}" -n - - 50 samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -n filt_aligned.bam
51 | bedtools bamtofastq -i /dev/stdin -fq multimap_1.fastq -fq2 multimap_2.fastq && 51 | bedtools bamtofastq -i /dev/stdin -fq multimap_1.fastq -fq2 multimap_2.fastq &&
52 #end if 52 #end if
53 samtools index unique.bam && 53 samtools index unique.bam &&
54 54
55 55