diff README.md @ 0:14fd6f3b0898 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty

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+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
+```