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annotate test-data/gen.sh @ 0:49a1cbbe5767 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
author iuc
date Wed, 12 Nov 2025 12:03:46 +0000
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49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
1 echo "> host" > host.fa
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
2 head -c 10000000 /dev/urandom | tr -dc 'ACGT' | head -c 100000 >> host.fa
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
3 echo "> contaminant" > contaminant.fa
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
4 head -c 10000000 /dev/urandom | tr -dc 'ACGT' | head -c 100000 >> contaminant.fa
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
6 art_illumina -ss HS25 -i host.fa -p -l 75 -f 1 -m 200 -s 10 -o host.fq
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
7 art_illumina -ss HS25 -i contaminant.fa -p -l 75 -f 1 -m 200 -s 10 -o contaminant.fq
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
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9 cat host.fq1.fq contaminant.fq1.fq > host_and_contaminant.fq1.fq
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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10 cat host.fq2.fq contaminant.fq2.fq > host_and_contaminant.fq2.fq
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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12 gzip -c host_and_contaminant.fq1.fq > host_and_contaminant.fq1.fq.gz
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
13 gzip -c host_and_contaminant.fq2.fq > host_and_contaminant.fq2.fq.gz
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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15 # use 10-mers to reduce size
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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16 bmtool -d host.fa -o host.bitmask -w 10
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
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17 srprism mkindex -i host.fa -o host.srprism
49a1cbbe5767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger commit e3d492d96b0ffe79370ca090b3f749b0869e8b60
iuc
parents:
diff changeset
18 makeblastdb -in host.fa -dbtype nucl