Mercurial > repos > bebatut > extract_sequence_file
changeset 1:bbde61ab5519 draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
| author | bebatut |
|---|---|
| date | Tue, 12 Apr 2016 02:59:22 -0400 |
| parents | 14fd6f3b0898 |
| children | |
| files | README.md |
| diffstat | 1 files changed, 0 insertions(+), 46 deletions(-) [+] |
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--- a/README.md Wed Jan 27 02:50:51 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -Extract from sequence file -========================== - -This tool is developped to extract from sequence file. Different treatments are possible. -Specific sequences could be extracted given some constraints and they could be saved in a sequence file. -Some information about the sequences such as the identifiant or the length could be extracted and saved in -a text file. Fastq file could also be split into a sequence file and a quality file. - -# Usage - -``` -python extract_sequence_file.py \ - --input input_sequence_filepath \ - --format fastq/fasta - --custom_extraction_type yes/no \ - [--output_sequence output_sequence_filepath if custom_extraction_type = no] \ - [--output_information information_filepath if custom_extraction_type = yes] \ - [--to_extract "{info_to_extract,info_to_extract}" if custom_extraction_type = yes] \ - [--split yes/no if format=fastq] \ - [--output_quality output_quality_filepath if split=yes] \ - [--quality_format sanger/solexa/illumina_1_3/illumina_1_5/illumina_1_8 if split=yes] \ - --report report_filepath \ - [--constraint info_to_constrain: type_of_constraint: value_of_constraint ] -``` -# Formats - -Formats for sequence file: - -- fasta -- fastq - -Formats for quality scores: - -- sanger -- solexa -- illumina_1_3 -- illumina_1_5 -- illumina_1_8 - -# Functional tests - -Some functional tests are implemented tot est the major treatments. To launch functional tests: - -``` -test-data/src/run_tests.sh -```