Increase documentation.

workflows/components/flash.py

@@ -31,8 +31,9 @@ import jflow.seqio as seqio
 class Flash (Analysis):
     def _get_length_table(self, input_file):
         """
-          @param input_file  : the fastq file path
-          @return            : [nb_seq, {size: nb, size:...}]
+          @param input_file : [str] the fastq file path
+          @return : [list] the number of sequences and the number of fragment by size. 
+                     Format : [nb_seq, {size_x: nb_fragment, size_j:...}]
         """       
         nb_seq = 0
         reader = seqio.SequenceReader(input_file)
@@ -48,17 +49,17 @@ class Flash (Analysis):
     def define_parameters(self, read1_files, read2_files, mismatch_ratio=None, min_overlap=None, max_overlap=None, avg_reads_length=None, avg_fragment_length=None, 
                           standard_deviation=None, phred_offset=None, nb_thread=1, archive_name=None):
         """
-          @param read1_files : paths to reads 1
-          @param read2_files : paths to reads 2
-          @param mismatch_ratio : maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value
-          @param min_overlap : the minimum required overlap length between two reads to provide a confident overlap
-          @param max_overlap : maximum overlap length expected in approximately 90% of read pairs
-          @param avg_reads_length : average read length
-          @param avg_fragment_length : average fragment length
-          @param standard_deviation : average fragment standard deviation
-          @param phred_offset : the smallest ASCII value of the characters used to represent quality values of bases in FASTQ files
-          @param nb_thread : set the number of worker threads
-          @param archive_name : name for the output archive
+          @param read1_files : [list] paths to reads 1
+          @param read2_files : [list] paths to reads 2
+          @param mismatch_ratio : [float] maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value
+          @param min_overlap : [int] the minimum required overlap length between two reads to provide a confident overlap
+          @param max_overlap : [int] maximum overlap length expected in approximately 90% of read pairs
+          @param avg_reads_length : [int] average read length
+          @param avg_fragment_length : [int] average fragment length
+          @param standard_deviation : [int] average fragment standard deviation
+          @param phred_offset : [int] the smallest ASCII value of the characters used to represent quality values of bases in FASTQ files
+          @param nb_thread : [int] set the number of worker threads
+          @param archive_name : [str] name for the output archive
         """
         self.read1_files = InputFileList(read1_files)#, Formats.FASTQ)
         self.read2_files = InputFileList(read2_files)#, Formats.FASTQ)