Mercurial > repos > greg > multigps
comparison multigps.xml @ 43:181076e82999 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Feb 2017 13:29:45 -0500 |
| parents | 8d30aeacb52a |
| children | d1a381f360f6 |
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| 42:8d30aeacb52a | 43:181076e82999 |
|---|---|
| 12 mkdir -p $output_dir && | 12 mkdir -p $output_dir && |
| 13 multigps | 13 multigps |
| 14 ############################ | 14 ############################ |
| 15 ## General options | 15 ## General options |
| 16 ############################ | 16 ############################ |
| 17 ## Append .txt extensions to events hrefs | |
| 18 ## in output dataset so files will render | |
| 19 ## in the browser. | |
| 20 --eventsaretxt | |
| 17 --expt '$expt' | 21 --expt '$expt' |
| 18 --format $expt.ext | 22 --format $expt.ext |
| 19 #if str($ctrl) != 'None': | 23 #if str($ctrl) != 'None': |
| 20 --ctrl '$ctrl' | 24 --ctrl '$ctrl' |
| 21 #end if | 25 #end if |
| 36 #set sdc = $aoc.scale_data_cond | 40 #set sdc = $aoc.scale_data_cond |
| 37 #set umc = $aoc.use_motif_cond | 41 #set umc = $aoc.use_motif_cond |
| 38 #if str($umc.use_motif) == 'yes': | 42 #if str($umc.use_motif) == 'yes': |
| 39 #set rgc = $umc.reference_genome_cond | 43 #set rgc = $umc.reference_genome_cond |
| 40 #if str($rgc.reference_genome_source) == 'cached': | 44 #if str($rgc.reference_genome_source) == 'cached': |
| 41 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] | 45 #set seq = '$rgc.reference_genome.fields.path' |
| 42 #else: | 46 #else: |
| 43 ## MultiGPS requires a directory containing reference files, so symlink the history dataset. | 47 #set seq = '$rgc.reference_genome' |
| 44 #import os | 48 #end if |
| 45 #import tempfile | 49 --seq $seq |
| 46 #set seq_dir = tempfile.mkdtemp(prefix='tmp-multigps-seq-dir') | |
| 47 #set seq_file = str($rgc.reference_genome) | |
| 48 #set tmp_filename = '%s.fa' % str($rgc.reference_genome.dbkey) | |
| 49 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename) | |
| 50 ln -f -s $tmp_seq_file $seq_file && | |
| 51 #end if | |
| 52 --seq $seq_dir | |
| 53 #end if | 50 #end if |
| 54 ############################ | 51 ############################ |
| 55 ## Limits on how many reads | 52 ## Limits on how many reads |
| 56 ############################ | 53 ############################ |
| 57 #if str($rloc.reads_limits) == 'yes': | 54 #if str($rloc.reads_limits) == 'yes': |