Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/srf2fastq.sh @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 #!/bin/sh |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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2 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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3 #change this if the path is different |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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4 convert=/usr/local/bin/srf2fastq |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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5 |
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6 srf_file=$1 |
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7 use_filter=$2 |
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8 use_paired=$3 |
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9 fastq_file1=$4 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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10 fastq_file2=$5 |
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11 options='-c ' |
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12 |
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13 if [ $use_filter == 'Y' ] |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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14 then |
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15 options="$options -C" |
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16 fi |
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17 |
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18 if [ $use_paired == 'Y' ] |
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19 then |
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20 options="$options -n -a -s ${fastq_file1}" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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21 ${convert} ${options} ${srf_file} |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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22 #after conversion rename files |
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23 mv ${fastq_file1}_1.fastq ${fastq_file1} |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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24 mv ${fastq_file1}_2.fastq ${fastq_file2} |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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25 else |
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26 ${convert} ${options} ${srf_file} > ${fastq_file1} |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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27 fi |
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28 |