# HG changeset patch # User devteam # Date 1506797887 14400 # Node ID 71e5fa25b8a24c94044235248264ddc9d82496c2 # Parent e4d28c94242d95e32103f3268c9e79c08c799f8f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a diff -r e4d28c94242d -r 71e5fa25b8a2 fastq_groomer.py --- a/fastq_groomer.py Wed Nov 11 12:40:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -#Dan Blankenberg -import sys -from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter - -def main(): - input_filename = sys.argv[1] - input_type = sys.argv[2] - output_filename = sys.argv[3] - output_type = sys.argv[4] - force_quality_encoding = sys.argv[5] - summarize_input = sys.argv[6] == 'summarize_input' - if force_quality_encoding == 'None': - force_quality_encoding = None - - aggregator = fastqAggregator() - out = fastqWriter( open( output_filename, 'wb' ), format = output_type, force_quality_encoding = force_quality_encoding ) - read_count = None - if summarize_input: - reader = fastqVerboseErrorReader - else: - reader = fastqReader - for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type, apply_galaxy_conventions = True ) ): - if summarize_input: - aggregator.consume_read( fastq_read ) - out.write( fastq_read ) - out.close() - - if read_count is not None: - print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type ) - if input_type != output_type and 'solexa' in [ input_type, output_type ]: - print "Converted between Solexa and PHRED scores." - if summarize_input: - print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) - ascii_range = aggregator.get_ascii_range() - decimal_range = aggregator.get_decimal_range() - print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed - print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) - else: - print "No valid FASTQ reads were provided." - - -if __name__ == "__main__": main() diff -r e4d28c94242d -r 71e5fa25b8a2 fastq_groomer.xml --- a/fastq_groomer.xml Wed Nov 11 12:40:56 2015 -0500 +++ b/fastq_groomer.xml Sat Sep 30 14:58:07 2017 -0400 @@ -1,342 +1,377 @@ - - convert between various FASTQ quality formats - - galaxy_sequence_utils - - fastq_groomer.py '$input_file' '$input_type' '$output_file' -#if str( $options_type['options_type_selector'] ) == 'basic': -#if str( $input_type ) == 'cssanger': -'cssanger' + + convert between various FASTQ quality formats + + galaxy_sequence_utils + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ | | | | | | 33 59 64 73 104 126 - + S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads) I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads) X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads) @@ -367,12 +402,9 @@ ------ - -.. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970 - - - - 10.1093/bioinformatics/btq281 - - +.. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: https://doi.org/10.1093/nar/gkp1137 + ]]> + + 10.1093/bioinformatics/btq281 + diff -r e4d28c94242d -r 71e5fa25b8a2 test-data/sanger_full_range_as_cssanger.fastqcssanger.bz2 Binary file test-data/sanger_full_range_as_cssanger.fastqcssanger.bz2 has changed diff -r e4d28c94242d -r 71e5fa25b8a2 test-data/sanger_full_range_original_sanger.fastqsanger.gz Binary file test-data/sanger_full_range_original_sanger.fastqsanger.gz has changed diff -r e4d28c94242d -r 71e5fa25b8a2 tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:40:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -