# HG changeset patch
# User bebatut
# Date 1460444362 14400
# Node ID bbde61ab5519bff28145f3d6ea33e9850a0eed94
# Parent  14fd6f3b0898721a1139973a3923352c9bcc1e3e
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty

diff -r 14fd6f3b0898 -r bbde61ab5519 README.md
--- 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
-```