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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 18b0b149cdda97c8d01caeb6debb77002a3ac89f
author drosofff
date Wed, 31 May 2017 16:51:37 -0400
parents 89968ee4bf95
children
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89968ee4bf95 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents: 0
diff changeset
1 input_base=Samp
89968ee4bf95 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents: 0
diff changeset
2 baseReference=chrM
0
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
3
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
4 bowtie-build ${baseReference}.fa ${baseReference}
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
5
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
6 python RepEnrich_setup.py ${baseReference}_repeatmasker.txt ${baseReference}.fa \
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
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7 setup_folder_${baseReference}
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
8
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
9 bowtie $baseReference -p 16 -t -m 1 -S --max ${input_base}_multimap.fastq \
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
10 ${input_base}.fastq ${input_base}_unique.sam
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
11
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
12 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
13 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
14 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
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15 samtools index ${input_base}_unique.bam
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
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16 rm ${input_base}_unique.sam
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
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041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
18 python RepEnrich.py ${baseReference}_repeatmasker.txt ${input_base} ${input_base} \
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
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19 setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus 16