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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
author bebatut
date Wed, 27 Jan 2016 02:50:51 -0500
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14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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1 Extract from sequence file
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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2 ==========================
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14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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4 This tool is developped to extract from sequence file. Different treatments are possible.
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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5 Specific sequences could be extracted given some constraints and they could be saved in a sequence file.
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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6 Some information about the sequences such as the identifiant or the length could be extracted and saved in
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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7 a text file. Fastq file could also be split into a sequence file and a quality file.
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9 # Usage
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11 ```
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12 python extract_sequence_file.py \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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13 --input input_sequence_filepath \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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14 --format fastq/fasta
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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15 --custom_extraction_type yes/no \
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16 [--output_sequence output_sequence_filepath if custom_extraction_type = no] \
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17 [--output_information information_filepath if custom_extraction_type = yes] \
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18 [--to_extract "{info_to_extract,info_to_extract}" if custom_extraction_type = yes] \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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19 [--split yes/no if format=fastq] \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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20 [--output_quality output_quality_filepath if split=yes] \
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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21 [--quality_format sanger/solexa/illumina_1_3/illumina_1_5/illumina_1_8 if split=yes] \
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22 --report report_filepath \
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23 [--constraint info_to_constrain: type_of_constraint: value_of_constraint ]
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24 ```
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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25 # Formats
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27 Formats for sequence file:
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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29 - fasta
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30 - fastq
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32 Formats for quality scores:
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34 - sanger
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35 - solexa
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36 - illumina_1_3
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37 - illumina_1_5
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38 - illumina_1_8
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40 # Functional tests
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42 Some functional tests are implemented tot est the major treatments. To launch functional tests:
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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44 ```
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45 test-data/src/run_tests.sh
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46 ```