# HG changeset patch # User devteam # Date 1506794044 14400 # Node ID b849e7c23b435b7a24b657b9e8fff3e02d10dd09 # Parent fdff6f6a8763cfc6dcff42cbbc17a48b51417265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a diff -r fdff6f6a8763 -r b849e7c23b43 fastq_trimmer.py --- a/fastq_trimmer.py Fri Dec 18 19:31:05 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -#Dan Blankenberg -import sys -from galaxy_utils.sequence.fastq import fastqReader, fastqWriter - -def main(): - input_filename = sys.argv[1] - output_filename = sys.argv[2] - left_offset = sys.argv[3] - right_offset = sys.argv[4] - percent_offsets = sys.argv[5] == 'offsets_percent' - input_type = sys.argv[6] or 'sanger' - keep_zero_length = sys.argv[7] == 'keep_zero_length' - - out = fastqWriter( open( output_filename, 'wb' ), format = input_type ) - num_reads_excluded = 0 - num_reads = None - for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): - if percent_offsets: - left_column_offset = int( round( float( left_offset ) / 100.0 * float( len( fastq_read ) ) ) ) - right_column_offset = int( round( float( right_offset ) / 100.0 * float( len( fastq_read ) ) ) ) - else: - left_column_offset = int( left_offset ) - right_column_offset = int( right_offset ) - if right_column_offset != 0: - right_column_offset = -right_column_offset - else: - right_column_offset = None - fastq_read = fastq_read.slice( left_column_offset, right_column_offset ) - if keep_zero_length or len( fastq_read ): - out.write( fastq_read ) - else: - num_reads_excluded += 1 - out.close() - if num_reads is None: - print "No valid fastq reads could be processed." - else: - print "%i fastq reads were processed." % ( num_reads + 1 ) - if num_reads_excluded: - print "%i reads of zero length were excluded from the output." % num_reads_excluded - -if __name__ == "__main__": main() diff -r fdff6f6a8763 -r b849e7c23b43 fastq_trimmer.xml --- a/fastq_trimmer.xml Fri Dec 18 19:31:05 2015 -0500 +++ b/fastq_trimmer.xml Sat Sep 30 13:54:04 2017 -0400 @@ -1,124 +1,112 @@ - - by column - - galaxy_sequence_utils - - fastq_trimmer.py '$input_file' '$output_file' '${offset_type['left_column_offset']}' '${offset_type['right_column_offset']}' '${offset_type['base_offset_type']}' '${input_file.extension[len( 'fastq' ):]}' '$keep_zero_length' - - - - - - - - - - - int( float( value ) ) == float( value ) - - - int( float( value ) ) == float( value ) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + by column + + galaxy_sequence_utils + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CBA@>7@7BBCA4-48%<;;%CBA@>7@7BBCA4-4 + Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: - + @Some FASTQ Sanger Read ATATGTNCTCACTGATAAGTGGATATN + - @.@;B-%?8>CBA@>7@7BBCA4-48% - + @.@;B-%?8>CBA@>7@7BBCA4-48% + ----- .. class:: warningmark Trimming a color space read will cause any adapter base to be lost. - ------- - - - - - 10.1093/bioinformatics/btq281 - - + ]]> + + 10.1093/bioinformatics/btq281 + diff -r fdff6f6a8763 -r b849e7c23b43 tool_dependencies.xml --- a/tool_dependencies.xml Fri Dec 18 19:31:05 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -