Mercurial > repos > tiagoantao > clone_filter
changeset 8:a8b87bc0c3ad draft
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty
| author | tiagoantao |
|---|---|
| date | Thu, 04 Feb 2016 08:13:32 -0500 |
| parents | 2059c028c07a |
| children | 89b911668f1d |
| files | STACKS_clone_filter.py STACKS_clone_filter.xml |
| diffstat | 2 files changed, 21 insertions(+), 6 deletions(-) [+] |
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--- a/STACKS_clone_filter.py Thu Feb 04 08:00:32 2016 -0500 +++ b/STACKS_clone_filter.py Thu Feb 04 08:13:32 2016 -0500 @@ -10,10 +10,19 @@ def __main__(): parser = argparse.ArgumentParser() + + #files (single or pair) parser.add_argument('-f', type=str) parser.add_argument('-fwd', type=str) parser.add_argument('-rev', type=str) + #oligos + parser.add_argument('-oligo_len_1', type=int) + parser.add_argument('-oligo_len_2', type=int) + + #options (allways there) + parser.add_argument('-opt', type=str) + #parser.add_argument('-k', action='store_true') options = parser.parse_args() @@ -30,6 +39,12 @@ cmd_line.extend(['-1', options.fwd]) cmd_line.extend(['-2', options.rev]) + if options.oligo_len_1 > -1: + cmd_line.extend(['--oligo_len_1', options.oligo_len_1]) + if options.oligo_len_2 > -1: + cmd_line.extend(['--oligo_len_2', options.oligo_len_2]) + cmd_line.append('--' + options.oligo_len_2) + print "[CMD]:"+' '.join(cmd_line) subprocess.call(cmd_line)
--- a/STACKS_clone_filter.xml Thu Feb 04 08:00:32 2016 -0500 +++ b/STACKS_clone_filter.xml Thu Feb 04 08:13:32 2016 -0500 @@ -18,7 +18,7 @@ -fwd $data_type.fwd -rev $data_type.rev #end if - $oligo_options + -opt $oligo_option #if $oligo_len_1 > -1: --oligo_len_1 $oligo_len_1 #end if @@ -44,11 +44,11 @@ <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/> <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/> <param name="oligo_options" type="select" label="Oligo sequence options"> - <option value="--inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option> - <option value="--null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> - <option value="--index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> - <option value="--inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> - <option value="--index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> + <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option> + <option value="null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> + <option value="index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> + <option value="inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> + <option value="index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> <option value="index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option> </param>