Mercurial > repos > drosofff > repenrich

annotate test-data/tool_wrapper.sh @ 1:fa1e919fafed draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e33b21484507981c2b8627a75cc5da3c1995b64a-dirty
author drosofff
date Tue, 23 May 2017 09:04:16 -0400
parents 041de602103e
children 89968ee4bf95
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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
1 input_base=$1
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
diff changeset
2 baseReference=$2
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:
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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:
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041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
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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:
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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:
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041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
drosofff
parents:
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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
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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:
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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:
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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