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comparison multigps.xml @ 43:181076e82999 draft

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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':