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comparison multigps.xml @ 20:0ea6413d66b2 draft

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Uploaded
author greg
date Tue, 13 Dec 2016 13:20:28 -0500
parents e3d9e74cae68
children 6ded14465b74
comparison
equal deleted inserted replaced
19:fc857bf96781 20:0ea6413d66b2
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 ## java -Xmx15G org.seqcode.projects.multigps.MultiGPS
11 ## --species "Saccharomyces cerevisiae;sacCer3"
12 ## --threads 2
13 ## --expt $bampath/$name.bam
14 ## --ctrl $control
15 ## --format BAM
16 ## --scalewin 500
17 ## --q 0.05
18 ## --nodifftests
19 ## --verbose
20 ## --mappability
21 ## --jointinmodel
22 ## --fixedmodelrange
23 ## --gaussmodelsmoothing
24 ## --gausssmoothparam 1
25 ## --minmodelupdateevents 50
26 ## --memepath $memePath
27 ## --mememinw 6
28 ## --mememaxw 18
29 ## --seq $genome
30 ## --exclude $exclude
31 ## --out $name > $name.out 2>&1
32 ##
33
34 multigps 10 multigps
35 ############################ 11 ############################
36 ## General options 12 ## General options
37 ############################ 13 ############################
38 --input "$input" 14 --input "$input"
61 #if str($rloc.nonunique) == "yes": 37 #if str($rloc.nonunique) == "yes":
62 --nonunique 38 --nonunique
63 #end if 39 #end if
64 --mappability $rloc.mappability 40 --mappability $rloc.mappability
65 #end if 41 #end if
66 #if str($rloc.nocache) == "yes": 42 #if str($rloc.nocache) == "yes":
67 --nocache 43 --nocache
68 #end if 44 #end if
69 ############################ 45 ############################
70 ## Scaling data 46 ## Scaling data
71 ############################ 47 ############################
72 #if str($sdc.scale_data) == "yes": 48 #if str($sdc.scale_data) == 'yes':
73 #if str($sdc.scaling) == 'no': 49 #if str($sdc.scaling) == 'no':
74 --noscaling $sdc.scaling 50 --noscaling $sdc.scaling
75 #end if 51 #end if
76 #if str($sdc.medianscale) == 'yes': 52 #if str($sdc.medianscale) == 'yes':
77 --medianscale $sdc.medianscale 53 --medianscale $sdc.medianscale
78 #end if 54 #end if
79 #if str($sdc.regressionscale) == 'yes': 55 #if str($sdc.regressionscale) == 'yes':
80 --regressionscale $sdc.regressionscale 56 --regressionscale $sdc.regressionscale
81 #endif 57 #enf if
82 #if str($sdc.sessscale) == 'yes': 58 #if str($sdc.sessscale) == 'yes':
83 --sesscale $sdc.sesscale 59 --sesscale $sdc.sesscale
84 #end if 60 #end if
85 #if $sdc.fixedscaling > 0: 61 #if $sdc.fixedscaling > 0:
86 ‒‒fixedscaling $sdc.fixedscaling 62 ‒‒fixedscaling $sdc.fixedscaling
91 #end if 67 #end if
92 #end if 68 #end if
93 ############################ 69 ############################
94 ## Running MultiGPS 70 ## Running MultiGPS
95 ############################ 71 ############################
96 #if str($aoc.nomodelupdate) == "no": 72 #if str($aoc.nomodelupdate) == 'no':
97 --nomodelupdate 73 --nomodelupdate
98 #end if 74 #end if
99 --minmodelupdateevents $aoc.minmodelupdateevents 75 --minmodelupdateevents $aoc.minmodelupdateevents
100 #if str($bmsc.nomodelsmoothing) == "no": 76 #if str($bmsc.nomodelsmoothing) == 'no':
101 --nomodelsmoothing 77 --nomodelsmoothing
102 #end if 78 #end if
103 --splinesmoothparam $aoc.splinesmoothparam 79 --splinesmoothparam $aoc.splinesmoothparam
104 #if str($gmsc.gaussmodelsmoothing) == "yes": 80 #if str($gmsc.gaussmodelsmoothing) == 'yes':
105 --gaussmodelsmoothing 81 --gaussmodelsmoothing
106 --gausssmoothparam $gmsc.gausssmoothparam 82 --gausssmoothparam $gmsc.gausssmoothparam
107 #end if 83 #end if
108 #if str($aoc.jointinmodel) == "yes": 84 #if str($aoc.jointinmodel) == 'yes':
109 --jointinmodel 85 --jointinmodel
110 #end if 86 #end if
111 #if str($aoc.fixedmodelrange) == "yes": 87 #if str($aoc.fixedmodelrange) == 'yes':
112 --fixedmodelrange 88 --fixedmodelrange
113 #end if 89 #end if
114 --prlogconf $aoc.prlogconf 90 --prlogconf $aoc.prlogconf
115 #if $aoc.fixedalpha > 0: 91 #if $aoc.fixedalpha > 0:
116 --fixedalpha $aoc.fixedalpha 92 --fixedalpha $aoc.fixedalpha
117 #end if 93 #end if
118 --alphascale $aoc.alphascale 94 --alphascale $aoc.alphascale
119 #if str($aoc.mlconfignotshared) == "no": 95 #if str($aoc.mlconfignotshared) == 'no':
120 --mlconfignotshared 96 --mlconfignotshared
121 #end if 97 #end if
122 --exclude "$aoc.exclude" 98 --exclude "$aoc.exclude"
123 ############################ 99 ############################
124 ## MultiGPS priors 100 ## MultiGPS priors
125 ############################ 101 ############################
126 #if str($umc.use_motif) == "yes": 102 #if str($umc.use_motif) == 'yes':
127 #set rgc = $umc.reference_genome_cond 103 #set rgc = $umc.reference_genome_cond
128 #if str($rgc.reference_genome_source) == "cached": 104 #if str($rgc.reference_genome_source) == "cached":
129 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] 105 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
130 #else: 106 #else:
131 ## MultiGPS requires a directory containing reference files, so symlink the history dataset. 107 ## MultiGPS requires a directory containing reference files, so symlink the history dataset.
138 ln -f -s $tmp_seq_file $seq_file && 114 ln -f -s $tmp_seq_file $seq_file &&
139 #end if 115 #end if
140 #set mpc = $umc.multigps_priors_cond 116 #set mpc = $umc.multigps_priors_cond
141 --seq $seq_dir 117 --seq $seq_dir
142 --geninfo ${chromInfo} 118 --geninfo ${chromInfo}
143 #if str($mpc.multigps_priors) == "yes": 119 #if str($mpc.multigps_priors) == 'yes':
144 #set bmc = $mpc.both_motifs_cond 120 #set bmc = $mpc.both_motifs_cond
145 #if str($mpc.noposprior) == "no": 121 #if str($mpc.noposprior) == 'no':
146 --noposprior 122 --noposprior
147 #end if 123 #end if
148 --probshared $mpc.probshared 124 --probshared $mpc.probshared
149 #if str($bmc.nomotifs) == "yes": 125 #if str($bmc.nomotifs) == 'yes':
150 --memenmotifs $bmc.memenmotifs 126 --memenmotifs $bmc.memenmotifs
151 --mememinw $bmc.mememinw 127 --mememinw $bmc.mememinw
152 --mememaxw $bmc.mememaxw 128 --mememaxw $bmc.mememaxw
153 #else: 129 #else:
154 --nomotifs 130 --nomotifs
155 #set mfoc = $bmc.nomotifprior_cond 131 #set mfoc = $bmc.nomotifprior_cond
156 --nomotifprior $mfoc.nomotifprior 132 --nomotifprior $mfoc.nomotifprior
157 #if str($mfoc.nomotifprior) == "yes": 133 #if str($mfoc.nomotifprior) == 'yes':
158 --memenmotifs $mfoc.memenmotifs 134 --memenmotifs $mfoc.memenmotifs
159 --mememinw $mfoc.mememinw 135 --mememinw $mfoc.mememinw
160 --mememaxw $mfoc.mememaxw 136 --mememaxw $mfoc.mememaxw
161 #end if 137 #end if
162 #end if 138 #end if
163 #end if 139 #end if
164 #end if 140 #end if
165 ############################ 141 ############################
166 ## Reporting binding events 142 ## Reporting binding events
167 ############################ 143 ############################
168 #if str($rbec.report_binding_events) == "yes": 144 #if str($rbec.report_binding_events) == 'yes':
169 --q $rbec.minqvalue 145 --q $rbec.minqvalue
170 --minfold $rbec.minfold 146 --minfold $rbec.minfold
171 #if str($rbec.nodifftests) == "no": 147 #if str($rbec.nodifftests) == 'no':
172 --nodifftests 148 --nodifftests
173 #end if 149 #end if
174 --edgerod $rbec.edgerod 150 --edgerod $rbec.edgerod
175 --diffp $rbec.diffp 151 --diffp $rbec.diffp
176 #end if 152 #end if
177 #end if 153 #end if
178 --out "$output_html.files_path" 154 --out "$output_html.files_path"
179 > "$output_html" 155 > "$output_html"
180 ##if str($output_process_log) == "yes": 156 ##if str($output_process_log) == 'yes':
181 ## --output_process_path "$output_process" 157 ## --output_process_path "$output_process"
182 ###end if 158 ###end if
183 ]]> 159 ]]>
184 </command> 160 </command>
185 <inputs> 161 <inputs>