Help getting fastq_filter.py working on command line?

[hlyates]

I want to use galaxy's fastq_filter tool on the command line.

Basically, I already know what the inputs are required by fastq_filter.py, but not sure how to generate two of them.

After you read the python and xml file, you learn that it is expecting us to run a line something like this:

fastq_filter.py $input_file $fastq_filter_file $output_file $output_file.files_path '${input_file.extension[len( 'fastq' ):]}'

• $input_file
• $fastq_filter_file I don't know how to make this
• $output_file
• $output_file.files_path I don't know what this is or how to avoid it
• ${input_file.extension[len( 'fastq' ):]} Seems to be type check input file type ? Not going to worry about this for now

The fastq_filter.ply is interesting. In it it has something like

def fastq_read_pass_filter( fastq_read ):
     def mean( score_list ):
         return float( sum( score_list ) ) / float( len( score_list ) )
     if len( fastq_read ) < $min_size:
         return False
     if $max_size > 0 and len( fastq_read ) > $max_size:
         return False
     num_deviates = $max_num_deviants
     qual_scores = fastq_read.get_decimal_quality_scores()
     for qual_score in qual_scores:
         if qual_score < $min_quality or ( $max_quality > 0 and qual_score > $max_quality ):
             if num_deviates == 0:
                 return False
             else:
                 num_deviates -= 1
 #if not $paired_end:
     qual_scores_split = [ qual_scores ]
 #else:
     qual_scores_split = [ qual_scores[ 0:int( len( qual_scores ) / 2 ) ], qual_scores[ int( len( qual_scores ) / 2 ): ] ]
 #end if
 #for $fastq_filter in $fastq_filters:
     for split_scores in qual_scores_split:
         left_column_offset = $fastq_filter[ 'offset_type' ][ 'left_column_offset' ]
         right_column_offset = $fastq_filter[ 'offset_type' ][ 'right_column_offset' ]
 #if $fastq_filter[ 'offset_type' ]['base_offset_type'] == 'offsets_percent':
         left_column_offset = int( round( float( left_column_offset ) / 100.0 * float( len( split_scores ) ) ) )
         right_column_offset = int( round( float( right_column_offset ) / 100.0 * float( len( split_scores ) ) ) )
 #end if
         if right_column_offset > 0:
             split_scores = split_scores[ left_column_offset:-right_column_offset]
         else:
             split_scores = split_scores[ left_column_offset:]
         if split_scores: ##if a read doesn't have enough columns, it passes by default
             if not ( ${fastq_filter[ 'score_operation' ]}( split_scores ) $fastq_filter[ 'score_comparison' ] $fastq_filter[ 'score' ]  ):
                 return False
 #end for
     return True

Is that python? Is this how the xml turns user input into a filter script? I had someone suggest I use the galaxy api for this, but that might be just as much work to get set up as getting this script to run? I'm not opposed to it, but I want to the easy way out because this is the last galaxy tool I have to run in my analysis I think before I move on to other things.

Any help and assistance would be appreciated.

[maubp]

The development repository is here:

https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter

Correction: The code you quoted is from the <configfile> XML snippet, it is a Python-like templating language called Cheetah.