Mercurial > repos > iuc > prinseq
comparison prinseq.xml @ 1:6b865dde1baa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit af00d26844b62927fd13703cd58ea3c59cc8f708
| author | iuc |
|---|---|
| date | Sat, 21 Jan 2017 06:27:29 -0500 |
| parents | ba78b984a9eb |
| children | 74afc47f326c |
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| 0:ba78b984a9eb | 1:6b865dde1baa |
|---|---|
| 33 && | 33 && |
| 34 | 34 |
| 35 prinseq-lite.pl | 35 prinseq-lite.pl |
| 36 #if $seq_type.seq_type_opt == "single": | 36 #if $seq_type.seq_type_opt == "single": |
| 37 -fastq "$seq_type.input_singles" | 37 -fastq "$seq_type.input_singles" |
| 38 #if $seq_type.input_singles.ext == "fastqillumina": | 38 #if $seq_type.input_singles.is_of_type('fastqillumina'): |
| 39 -phred64 | 39 -phred64 |
| 40 #end if | 40 #end if |
| 41 #else: | 41 #else: |
| 42 -fastq "$seq_type.input_mate1" | 42 -fastq "$seq_type.input_mate1" |
| 43 -fastq2 "$seq_type.input_mate2" | 43 -fastq2 "$seq_type.input_mate2" |
| 44 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext: | 44 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext: |
| 45 #import sys | 45 #import sys |
| 46 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' ) | 46 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' ) |
| 47 #end if | 47 #end if |
| 48 #if $seq_type.input_mate1.ext == "fastqillumina": | 48 #if $seq_type.input_mate1.is_of_type('fastqillumina'): |
| 49 -phred64 | 49 -phred64 |
| 50 #end if | 50 #end if |
| 51 #end if | 51 #end if |
| 52 | 52 |
| 53 -out_good "tmp/good_sequences" | 53 -out_good "tmp/good_sequences" |