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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a |
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modified:
fastq_trimmer.xml |
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removed:
fastq_trimmer.py tool_dependencies.xml |
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| diff -r e0cfb5a703ce -r 430b9da91435 fastq_trimmer.py --- a/fastq_trimmer.py Wed Nov 11 12:42:58 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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() |
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| diff -r e0cfb5a703ce -r 430b9da91435 fastq_trimmer.xml --- a/fastq_trimmer.xml Wed Nov 11 12:42:58 2015 -0500 +++ b/fastq_trimmer.xml Sat Sep 30 13:55:56 2017 -0400 |
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| b'@@ -1,125 +1,112 @@\n-<tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0">\n- <description>by column</description>\n- <requirements>\n- <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>\n- </requirements>\n- <command interpreter="python">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\'</command>\n- <inputs>\n- <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/>\n- <conditional name="offset_type">\n- <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)">\n- <option value="offsets_absolute" selected="true">Absolute Values</option>\n- <option value="offsets_percent">Percentage of Read Length</option>\n- </param>\n- <when value="offsets_absolute">\n- <param name="left_column_offset" label="Offset from 5\' end" value="0" type="integer" help="Values start at 0, increasing from the left">\n- <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>\n- <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>\n- </param>\n- <param name="right_column_offset" label="Offset from 3\' end" value="0" type="integer" help="Values start at 0, increasing from the right">\n- <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>\n- <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>\n- </param>\n- </when>\n- <when value="offsets_percent">\n- <param name="left_column_offset" label="Offset from 5\' end" value="0" type="float">\n- <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/>\n- </param>\n- <param name="right_column_offset" label="Offset from 3\' end" value="0" type="float">\n- <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/>\n- </param>\n- </when>\n- </conditional>\n- <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/>\n- </inputs>\n- <outputs>\n- <data name="output_file" format="input" />\n- </outputs>\n- <tests>\n- <test>\n- <!-- Do nothing trim -->\n- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n- <param name="base_offset_type" value="offsets_absolute"/>\n- <param name="left_column_offset" value="0"/>\n- <param name="right_column_offset" value="0"/>\n- <param name="keep_zero_length" value="keep_zero_length" />\n- <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />\n- </test>\n- <!-- Trim to empty File -->\n- <test>\n- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n- <param name="base_offset_type" value="offsets_absolute"/>\n- <param name="left_column_offset" value="30"/>\n- <param name="right_column_offset" value="64"/>\n- <param name="keep_zero_length" value="exclude_zero_length" />\n- <output name="output_file" file="empty_file.dat" />\n- </test>\n- <test>\n- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n- <param name="base_offset_type" value="offsets_percent"/>\n- <param name="left_column_offset" value="50"/>\n- <param name="right_column_offset" value="50"/>\n- <param name="keep_zero_length" value="exclude_zero_length" />\n- <output name="output_'..b' <param name="left_column_offset" value="0"/>\n+ <param name="right_column_offset" value="0"/>\n+ <param name="keep_zero_length" value="keep_zero_length" />\n+ <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n+ </test>\n+ <!-- Trim to empty File -->\n+ <test>\n+ <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n+ <param name="base_offset_type" value="offsets_absolute"/>\n+ <param name="left_column_offset" value="30"/>\n+ <param name="right_column_offset" value="64"/>\n+ <param name="keep_zero_length" value="exclude_zero_length" />\n+ <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />\n+ </test>\n+ <test>\n+ <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n+ <param name="base_offset_type" value="offsets_percent"/>\n+ <param name="left_column_offset" value="50"/>\n+ <param name="right_column_offset" value="50"/>\n+ <param name="keep_zero_length" value="exclude_zero_length" />\n+ <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />\n+ </test>\n+ <!-- Trim to 4 inner-most bases -->\n+ <test>\n+ <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n+ <param name="base_offset_type" value="offsets_absolute"/>\n+ <param name="left_column_offset" value="45"/>\n+ <param name="right_column_offset" value="45"/>\n+ <param name="keep_zero_length" value="exclude_zero_length" />\n+ <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />\n+ </test>\n+ <test>\n+ <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n+ <param name="base_offset_type" value="offsets_percent"/>\n+ <param name="left_column_offset" value="47.87"/>\n+ <param name="right_column_offset" value="47.87"/>\n+ <param name="keep_zero_length" value="exclude_zero_length" />\n+ <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n **What is does**\n- \n+\n This tool allows you to trim the ends of reads.\n \n-You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer. \n+You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer.\n \n For example, if you have a read of length 36::\n- \n+\n @Some FASTQ Sanger Read\n CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA\n +\n- =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@\n- \n+ =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@\n+\n And you set absolute offsets of 2 and 9::\n- \n+\n @Some FASTQ Sanger Read\n ATATGTNCTCACTGATAAGTGGATA\n +\n- @.@;B-%?8>CBA@>7@7BBCA4-4\n- \n+ @.@;B-%?8>CBA@>7@7BBCA4-4\n+\n Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36)::\n- \n+\n @Some FASTQ Sanger Read\n ATATGTNCTCACTGATAAGTGGATATN\n +\n- @.@;B-%?8>CBA@>7@7BBCA4-48%\n- \n+ @.@;B-%?8>CBA@>7@7BBCA4-48%\n+\n -----\n \n .. class:: warningmark\n \n Trimming a color space read will cause any adapter base to be lost.\n-\n-------\n-\n- </help>\n- \n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btq281</citation>\n- </citations>\n- \n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btq281</citation>\n+ </citations>\n </tool>\n' |
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| diff -r e0cfb5a703ce -r 430b9da91435 tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:42:58 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="galaxy_sequence_utils" version="1.0.0"> - <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |