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1 #!/bin/sh
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2 ## same as galaxy terst
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3 ./paired_fastq_filtering_wrapper.sh -a test_data/ERR215189_1_part.fastq.gz -b test_data/ERR215189_2_part.fastq.gz -o test_data/single_output.fasta -G test_data/single_output.png -c 10 -N 0 -p 95
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4
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5 echo "paired fastq filtering with defaults"
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6 ./paired_fastq_filtering_wrapper.sh -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.1.fasta -G tmp/test2.1.png -c 10 -N 0
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7
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8 echo "paired fastq filtering with with sampling"
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5
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9 ./paired_fastq_filtering_wrapper.sh -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.a2.fasta -G tmp/test2.2.png -c 10 -N 0 -n 500
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10
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11 echo "paired fastq filtering with with sampling"
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12 ./paired_fastq_filtering_wrapper.sh -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.a3.fasta -G tmp/test2.2.png -c 10 -N 0 -n 653
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13
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14 echo "paired fastq filtering with with sampling"
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15 ./paired_fastq_filtering_wrapper.sh -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.a4.fasta -G tmp/test2.2.png -c 10 -N 0 -n 547
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16
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17 echo "paired fastq filtering with with sampling"
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18 ./paired_fastq_filtering_wrapper.sh -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.a5.fasta -G tmp/test2.2.png -c 10 -N 0 -n 839
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0
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19
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20 echo "paired fastq filtering with contaminant removing"
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21 ./paired_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.3.fasta -G tmp/test2.3.png -c 10 -N 0
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22
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23 echo "paired fastq filtering with contaminant removing + trimming"
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24 ./paired_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -b test_data/ERR215189_2_part.fastq.gz -a test_data/ERR215189_1_part.fastq.gz -o tmp/test2.3.fasta -G tmp/test2.3.png -c 10 -N 0 -s 10 -e 80
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25
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26
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27 echo "paired fastq filtering with contaminant removing - full run"
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28 ./paired_fastq_filtering_wrapper.sh -F tool_data/organele_ref_and_phi-X174.fasta -b test_data/ERR215189_2.fastq.gz -a test_data/ERR215189_1.fastq.gz -o tmp/test2.3.fasta -G tmp/test2.3.png -c 10 -N 0
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29
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