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comparison multigps.xml @ 31:71b0f24e12f6 draft

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Uploaded
author greg
date Wed, 14 Dec 2016 08:31:55 -0500
parents 9aca70ab05c2
children 7a5a2e70b588
comparison
equal deleted inserted replaced
30:9aca70ab05c2 31:71b0f24e12f6
30 #set gmsc = $aoc.gauss_model_smoothing_cond 30 #set gmsc = $aoc.gauss_model_smoothing_cond
31 #set rbec = $aoc.report_binding_events_cond 31 #set rbec = $aoc.report_binding_events_cond
32 #set rloc = $aoc.reads_limits_options_cond 32 #set rloc = $aoc.reads_limits_options_cond
33 #set sdc = $aoc.scale_data_cond 33 #set sdc = $aoc.scale_data_cond
34 #set umc = $aoc.use_motif_cond 34 #set umc = $aoc.use_motif_cond
35 ############################ 35 #if str($umc.use_motif) == "yes":
36 ## Limits on how many reads
37 ############################
38 #if str($rloc.reads_limits) == 'yes':
39 --fixedpb $rloc.fixedpb
40 --poissongausspb $rloc.poissongausspb
41 #if str($rloc.nonunique) == 'yes':
42 --nonunique
43 #end if
44 --mappability $rloc.mappability
45 #if str($rloc.nocache) == 'yes':
46 --nocache
47 #end if
48 #end if
49 ############################
50 ## Scaling data
51 ############################
52 #if str($sdc.scale_data) == 'yes':
53 #if str($sdc.scaling) == 'no':
54 --noscaling $sdc.scaling
55 #end if
56 #if str($sdc.medianscale) == 'yes':
57 --medianscale $sdc.medianscale
58 #end if
59 #if str($sdc.regressionscale) == 'yes':
60 --regressionscale $sdc.regressionscale
61 #end if
62 #if str($sdc.sesscale) == 'yes':
63 --sesscale $sdc.sesscale
64 #end if
65 #if $sdc.fixedscaling > 0:
66 ‒‒fixedscaling $sdc.fixedscaling
67 #end if
68 --scalewin $sdc.scalewin
69 #if str($sdc.plotscaling) == 'yes':
70 --plotscaling $sdc.plotscaling
71 #end if
72 #end if
73 ############################
74 ## Running MultiGPS
75 ############################
76 #if str($aoc.nomodelupdate) == 'no':
77 --nomodelupdate
78 #end if
79 --minmodelupdateevents $aoc.minmodelupdateevents
80 #if str($aoc.nomodelsmoothing) == 'no':
81 --nomodelsmoothing
82 #end if
83 --splinesmoothparam $aoc.splinesmoothparam
84 #if str($gmsc.gaussmodelsmoothing) == 'yes':
85 --gaussmodelsmoothing
86 --gausssmoothparam $gmsc.gausssmoothparam
87 #end if
88 #if str($aoc.jointinmodel) == 'yes':
89 --jointinmodel
90 #end if
91 #if str($aoc.fixedmodelrange) == 'yes':
92 --fixedmodelrange
93 #end if
94 --prlogconf $aoc.prlogconf
95 #if $aoc.fixedalpha > 0:
96 --fixedalpha $aoc.fixedalpha
97 #end if
98 --alphascale $aoc.alphascale
99 #if str($aoc.mlconfignotshared) == 'no':
100 --mlconfignotshared
101 #end if
102 --exclude "$aoc.exclude"
103 ############################
104 ## MultiGPS priors
105 ############################
106 #if str($umc.use_motif) == 'yes':
107 #set mpc = $umc.multigps_priors_cond
108 #set rgc = $umc.reference_genome_cond 36 #set rgc = $umc.reference_genome_cond
109 #if str($rgc.reference_genome_source) == "cached": 37 #if str($rgc.reference_genome_source) == "cached":
110 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] 38 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
111 #else: 39 #else:
112 ## MultiGPS requires a directory containing reference files, so symlink the history dataset. 40 ## MultiGPS requires a directory containing reference files, so symlink the history dataset.
116 #set seq_file = str($rgc.reference_genome) 44 #set seq_file = str($rgc.reference_genome)
117 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey) 45 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey)
118 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename) 46 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename)
119 ln -f -s $tmp_seq_file $seq_file && 47 ln -f -s $tmp_seq_file $seq_file &&
120 #end if 48 #end if
121 --seq $seq_dir 49 #end if
50 ############################
51 ## Limits on how many reads
52 ############################
53 #if str($rloc.reads_limits) == 'yes':
54 --fixedpb $rloc.fixedpb
55 --poissongausspb $rloc.poissongausspb
56 #if str($rloc.nonunique) == 'yes':
57 --nonunique
58 #end if
59 --mappability $rloc.mappability
60 #if str($rloc.nocache) == 'yes':
61 --nocache
62 #end if
63 #end if
64 ############################
65 ## Scaling data
66 ############################
67 #if str($sdc.scale_data) == 'yes':
68 #if str($sdc.scaling) == 'no':
69 --noscaling $sdc.scaling
70 #end if
71 #if str($sdc.medianscale) == 'yes':
72 --medianscale $sdc.medianscale
73 #end if
74 #if str($sdc.regressionscale) == 'yes':
75 --regressionscale $sdc.regressionscale
76 #end if
77 #if str($sdc.sesscale) == 'yes':
78 --sesscale $sdc.sesscale
79 #end if
80 #if $sdc.fixedscaling > 0:
81 ‒‒fixedscaling $sdc.fixedscaling
82 #end if
83 --scalewin $sdc.scalewin
84 #if str($sdc.plotscaling) == 'yes':
85 --plotscaling $sdc.plotscaling
86 #end if
87 #end if
88 ############################
89 ## Running MultiGPS
90 ############################
91 #if str($aoc.nomodelupdate) == 'no':
92 --nomodelupdate
93 #end if
94 --minmodelupdateevents $aoc.minmodelupdateevents
95 #if str($aoc.nomodelsmoothing) == 'no':
96 --nomodelsmoothing
97 #end if
98 --splinesmoothparam $aoc.splinesmoothparam
99 #if str($gmsc.gaussmodelsmoothing) == 'yes':
100 --gaussmodelsmoothing
101 --gausssmoothparam $gmsc.gausssmoothparam
102 #end if
103 #if str($aoc.jointinmodel) == 'yes':
104 --jointinmodel
105 #end if
106 #if str($aoc.fixedmodelrange) == 'yes':
107 --fixedmodelrange
108 #end if
109 --prlogconf $aoc.prlogconf
110 #if $aoc.fixedalpha > 0:
111 --fixedalpha $aoc.fixedalpha
112 #end if
113 --alphascale $aoc.alphascale
114 #if str($aoc.mlconfignotshared) == 'no':
115 --mlconfignotshared
116 #end if
117 --exclude "$aoc.exclude"
118 ############################
119 ## MultiGPS priors
120 ############################
121 #if str($umc.use_motif) == 'yes':
122 #set mpc = $umc.multigps_priors_cond
122 #if str($mpc.multigps_priors) == 'yes': 123 #if str($mpc.multigps_priors) == 'yes':
123 #set bmc = $mpc.both_motifs_cond 124 #set bmc = $mpc.both_motifs_cond
124 #if str($mpc.noposprior) == 'no': 125 #if str($mpc.noposprior) == 'no':
125 --noposprior 126 --noposprior
126 #end if 127 #end if