Mercurial > repos > greg > multigps

comparison multigps.xml @ 25:32a59270224b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 14 Dec 2016 07:54:08 -0500
parents d5c1ab05259b
children fcc1cc3f3e3c
comparison
equal deleted inserted replaced
24:d5c1ab05259b 25:32a59270224b
28 #set gmsc = $aoc.gauss_model_smoothing_cond 28 #set gmsc = $aoc.gauss_model_smoothing_cond
29 #set rbec = $aoc.report_binding_events_cond 29 #set rbec = $aoc.report_binding_events_cond
30 #set rloc = $aoc.reads_limits_options_cond 30 #set rloc = $aoc.reads_limits_options_cond
31 #set sdc = $aoc.scale_data_cond 31 #set sdc = $aoc.scale_data_cond
32 #set umc = $aoc.use_motif_cond 32 #set umc = $aoc.use_motif_cond
33 #set mpc = $umc.multigps_priors_cond
34 #set bmc = $mpc.both_motifs_cond
35 #set mfoc = $bmc.nomotifprior_cond
36 #set rgc = $umc.reference_genome_cond
37 #if str($aoc.advanced_options) == 'display': 33 #if str($aoc.advanced_options) == 'display':
38 ############################ 34 ############################
39 ## Limits on how many reads 35 ## Limits on how many reads
40 ############################ 36 ############################
41 #if str($rloc.reads_limits) == 'yes': 37 #if str($rloc.reads_limits) == 'yes':
105 --exclude "$aoc.exclude" 101 --exclude "$aoc.exclude"
106 ############################ 102 ############################
107 ## MultiGPS priors 103 ## MultiGPS priors
108 ############################ 104 ############################
109 #if str($umc.use_motif) == 'yes': 105 #if str($umc.use_motif) == 'yes':
106 #set mpc = $umc.multigps_priors_cond
107 #set rgc = $umc.reference_genome_cond
110 #if str($rgc.reference_genome_source) == "cached": 108 #if str($rgc.reference_genome_source) == "cached":
111 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] 109 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
112 #else: 110 #else:
113 ## MultiGPS requires a directory containing reference files, so symlink the history dataset. 111 ## MultiGPS requires a directory containing reference files, so symlink the history dataset.
114 #import os 112 #import os
120 ln -f -s $tmp_seq_file $seq_file && 118 ln -f -s $tmp_seq_file $seq_file &&
121 #end if 119 #end if
122 --seq $seq_dir 120 --seq $seq_dir
123 --geninfo ${chromInfo} 121 --geninfo ${chromInfo}
124 #if str($mpc.multigps_priors) == 'yes': 122 #if str($mpc.multigps_priors) == 'yes':
123 #set bmc = $mpc.both_motifs_cond
125 #if str($mpc.noposprior) == 'no': 124 #if str($mpc.noposprior) == 'no':
126 --noposprior 125 --noposprior
127 #end if 126 #end if
128 --probshared $mpc.probshared 127 --probshared $mpc.probshared
129 #if str($bmc.nomotifs) == 'yes': 128 #if str($bmc.nomotifs) == 'yes':
130 --memenmotifs $bmc.memenmotifs 129 --memenmotifs $bmc.memenmotifs
131 --mememinw $bmc.mememinw 130 --mememinw $bmc.mememinw
132 --mememaxw $bmc.mememaxw 131 --mememaxw $bmc.mememaxw
133 #else: 132 #else:
133 #set mfoc = $bmc.nomotifprior_cond
134 --nomotifs 134 --nomotifs
135 --nomotifprior $mfoc.nomotifprior 135 --nomotifprior $mfoc.nomotifprior
136 #if str($mfoc.nomotifprior) == 'yes': 136 #if str($mfoc.nomotifprior) == 'yes':
137 --memenmotifs $mfoc.memenmotifs 137 --memenmotifs $mfoc.memenmotifs
138 --mememinw $mfoc.mememinw 138 --mememinw $mfoc.mememinw