Mercurial > repos > devteam > fastq_paired_end_joiner
changeset 3:e659bd662045 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 06ff7f8972dcefaf52121c22ec82cf5d315adb3e-dirty
| author | devteam |
|---|---|
| date | Mon, 14 Dec 2015 16:03:18 -0500 |
| parents | ab37758348d0 |
| children | bce792b8e239 |
| files | fastq_paired_end_joiner.py fastq_paired_end_joiner.xml tool_dependencies.xml |
| diffstat | 3 files changed, 19 insertions(+), 12 deletions(-) [+] |
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--- a/fastq_paired_end_joiner.py Tue Oct 13 12:44:00 2015 -0400 +++ b/fastq_paired_end_joiner.py Mon Dec 14 16:03:18 2015 -0500 @@ -54,8 +54,8 @@ class FastqJoiner( fq.fastqJoiner ): - def __init__( self, format, force_quality_encoding=None, sep="\t" ): - super( FastqJoiner, self ).__init__( format, force_quality_encoding ) + def __init__( self, format, force_quality_encoding=None, sep="\t", paste="" ): + super( FastqJoiner, self ).__init__( format, force_quality_encoding, paste=paste ) self.id_manager = IDManager( sep ) def join( self, read1, read2 ): @@ -84,16 +84,20 @@ # convert to nuc space, join, then convert back rval.sequence = rval.convert_base_to_color_space( read1.convert_color_to_base_space( read1.sequence ) + + self.paste_sequence + read2.convert_color_to_base_space( read2.sequence ) ) else: - rval.sequence = read1.sequence + read2.sequence + rval.sequence = read1.sequence + self.paste_sequence + read2.sequence if force_quality_encoding == 'ascii': - rval.quality = read1.quality + read2.quality + rval.quality = read1.quality + self.paste_ascii_quality + read2.quality else: rval.quality = "%s %s" % ( - read1.quality.strip(), read2.quality.strip() + read1.quality.strip(), self.paste_decimal_quality ) + rval.quality = ("%s %s" % ( + rval.quality.strip(), read2.quality.strip() + )).strip() return rval def get_paired_identifier( self, read ): @@ -119,15 +123,17 @@ output_filename = sys.argv[5] fastq_style = sys.argv[6] or 'old' + + paste = sys.argv[7] or '' #-- if input1_type != input2_type: print "WARNING: You are trying to join files of two different types: %s and %s." % ( input1_type, input2_type ) if fastq_style == 'new': sep = sniff_sep( input1_filename ) - joiner = FastqJoiner( input1_type, sep=sep ) + joiner = FastqJoiner( input1_type, sep=sep, paste=paste ) else: - joiner = fq.fastqJoiner( input1_type ) + joiner = fq.fastqJoiner( input1_type, paste=paste ) #-- input2 = fq.fastqNamedReader( open( input2_filename, 'rb' ), input2_type ) out = fq.fastqWriter( open( output_filename, 'wb' ), format=input1_type )
--- a/fastq_paired_end_joiner.xml Tue Oct 13 12:44:00 2015 -0400 +++ b/fastq_paired_end_joiner.xml Mon Dec 14 16:03:18 2015 -0500 @@ -1,9 +1,9 @@ -<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.0"> +<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1"> <description>on paired end reads</description> <requirements> - <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> + <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> </requirements> - <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style'</command> + <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style' '${paste_sequence}'</command> <inputs> <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" /> <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" /> @@ -11,6 +11,7 @@ <option value="old" selected="true">old</option> <option value="new">new</option> </param> + <param name="paste_sequence" type="text" label="Bases to insert between joined reads" value="" help="Values are in Base-space and quality scores of maximal value will be used"/> </inputs> <outputs> <data name="output_file" format="input" />
--- a/tool_dependencies.xml Tue Oct 13 12:44:00 2015 -0400 +++ b/tool_dependencies.xml Mon Dec 14 16:03:18 2015 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="galaxy_sequence_utils" version="1.0.0"> - <repository changeset_revision="195699b1562a" name="package_galaxy_utils_1_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="galaxy_sequence_utils" version="1.0.1"> + <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>