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comparison multigps.xml @ 5:d7c4baf43c13 draft

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author iuc
date Tue, 04 Apr 2017 10:02:01 -0400
parents 0bec3b2df784
children 7dc47046b54c
comparison
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4:0bec3b2df784 5:d7c4baf43c13
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.74">multigps</requirement> 7 <requirement type="package" version="0.74">multigps</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 python $__tool_directory__/multigps.py 11 #set output_dir = $output_html.files_path
12 mkdir -p $output_dir &&
13 multigps
12 ## General options 14 ## General options
13 #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt 15 #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt
14 #if str($single_or_multi_expt) == 'multi': 16 #if str($single_or_multi_expt) == 'multi':
15 #for $i in $single_or_multi_expt_cond['input_items']: 17 #for $i in $single_or_multi_expt_cond['input_items']:
16 #set label_cond = $i['label_cond'] 18 #set label_cond = $i['label_cond']
42 #end if 44 #end if
43 #end if 45 #end if
44 ## Append .txt extensions to events hrefs 46 ## Append .txt extensions to events hrefs
45 ## in output dataset so files will render 47 ## in output dataset so files will render
46 ## in the browser. 48 ## in the browser.
47 --eventsaretxt 'true' 49 --eventsaretxt
48 ## Do not run the parallel version of meme. 50 ## Do not run the parallel version of meme.
49 --meme1proc 'true' 51 --meme1proc
50 --threads \${GALAXY_SLOTS:-4} 52 --threads \${GALAXY_SLOTS:-4}
51 --chrom_len_file '$chromInfo' 53 --geninfo '$chromInfo'
52 ## Advanced options 54 ## Advanced options
53 #set aoc = $advanced_options_cond 55 #set aoc = $advanced_options_cond
54 #if str($aoc.advanced_options) == 'display': 56 #if str($aoc.advanced_options) == 'display':
55 #set bmsc = $aoc.binding_model_smoothing_cond 57 #set bmsc = $aoc.binding_model_smoothing_cond
56 #set gmsc = $aoc.gauss_model_smoothing_cond 58 #set gmsc = $aoc.gauss_model_smoothing_cond
70 ## Limits on how many reads 72 ## Limits on how many reads
71 #if str($rloc.reads_limits) == 'yes': 73 #if str($rloc.reads_limits) == 'yes':
72 --fixedpb $rloc.fixedpb 74 --fixedpb $rloc.fixedpb
73 --poissongausspb $rloc.poissongausspb 75 --poissongausspb $rloc.poissongausspb
74 #if str($rloc.nonunique) == 'yes': 76 #if str($rloc.nonunique) == 'yes':
75 --nonunique 'true' 77 --nonunique
76 #end if 78 #end if
77 --mappability $rloc.mappability 79 --mappability $rloc.mappability
78 #if str($rloc.nocache) == 'yes': 80 #if str($rloc.nocache) == 'yes':
79 --nocache 'true' 81 --nocache
80 #end if 82 #end if
81 #end if 83 #end if
82 ## Scaling data 84 ## Scaling data
83 #if str($sdc.scale_data) == 'yes': 85 #if str($sdc.scale_data) == 'yes':
84 #if str($sdc.scaling) == 'no': 86 #if str($sdc.scaling) == 'no':
105 #if str($aoc.readdistributionfile) != 'None': 107 #if str($aoc.readdistributionfile) != 'None':
106 --readdistributionfile '$aoc.readdistributionfile' 108 --readdistributionfile '$aoc.readdistributionfile'
107 #end if 109 #end if
108 --maxtrainingrounds $aoc.maxtrainingrounds 110 --maxtrainingrounds $aoc.maxtrainingrounds
109 #if str($aoc.nomodelupdate) == 'no': 111 #if str($aoc.nomodelupdate) == 'no':
110 --nomodelupdate 'true' 112 --nomodelupdate
111 #end if 113 #end if
112 --minmodelupdateevents $aoc.minmodelupdateevents 114 --minmodelupdateevents $aoc.minmodelupdateevents
113 #if str($bmsc.nomodelsmoothing) == 'no': 115 #if str($bmsc.nomodelsmoothing) == 'no':
114 --nomodelsmoothing 'true' 116 --nomodelsmoothing
115 #else: 117 #else:
116 --splinesmoothparam $bmsc.splinesmoothparam 118 --splinesmoothparam $bmsc.splinesmoothparam
117 #end if 119 #end if
118 #if str($gmsc.gaussmodelsmoothing) == 'yes': 120 #if str($gmsc.gaussmodelsmoothing) == 'yes':
119 --gaussmodelsmoothing 'true' 121 --gaussmodelsmoothing
120 --gausssmoothparam $gmsc.gausssmoothparam 122 --gausssmoothparam $gmsc.gausssmoothparam
121 #end if 123 #end if
122 #if str($aoc.jointinmodel) == 'yes': 124 #if str($aoc.jointinmodel) == 'yes':
123 --jointinmodel 'true' 125 --jointinmodel
124 #end if 126 #end if
125 #if str($aoc.fixedmodelrange) == 'yes': 127 #if str($aoc.fixedmodelrange) == 'yes':
126 --fixedmodelrange 'true' 128 --fixedmodelrange
127 #end if 129 #end if
128 --prlogconf $aoc.prlogconf 130 --prlogconf $aoc.prlogconf
129 #if $aoc.fixedalpha > 0: 131 #if $aoc.fixedalpha > 0:
130 --fixedalpha $aoc.fixedalpha 132 --fixedalpha $aoc.fixedalpha
131 #end if 133 #end if
132 --alphascale $aoc.alphascale 134 --alphascale $aoc.alphascale
133 #if str($aoc.mlconfignotshared) == 'no': 135 #if str($aoc.mlconfignotshared) == 'no':
134 --mlconfignotshared 'true' 136 --mlconfignotshared
135 #end if 137 #end if
136 #if str($aoc.exclude) != 'None': 138 #if str($aoc.exclude) != 'None':
137 --exclude '$aoc.exclude' 139 --exclude '$aoc.exclude'
138 #end if 140 #end if
139 ## MultiGPS priors 141 ## MultiGPS priors
140 #if str($umc.use_motif) == 'yes': 142 #if str($umc.use_motif) == 'yes':
141 #set mpc = $umc.multigps_priors_cond 143 #set mpc = $umc.multigps_priors_cond
142 #if str($mpc.multigps_priors) == 'yes': 144 #if str($mpc.multigps_priors) == 'yes':
143 #set bmc = $mpc.both_motifs_cond 145 #set bmc = $mpc.both_motifs_cond
144 #if str($mpc.noposprior) == 'no': 146 #if str($mpc.noposprior) == 'no':
145 --noposprior 'true' 147 --noposprior
146 #end if 148 #end if
147 --probshared $mpc.probshared 149 --probshared $mpc.probshared
148 #if str($bmc.nomotifs) == 'yes': 150 #if str($bmc.nomotifs) == 'yes':
149 --memenmotifs $bmc.memenmotifs 151 --memenmotifs $bmc.memenmotifs
150 --mememinw $bmc.mememinw 152 --mememinw $bmc.mememinw
151 --mememaxw $bmc.mememaxw 153 --mememaxw $bmc.mememaxw
152 #else: 154 #else:
153 #set nmpc = $bmc.nomotifprior_cond 155 #set nmpc = $bmc.nomotifprior_cond
154 --nomotifs 'true' 156 --nomotifs
155 #if str($nmpc.nomotifprior) == 'yes': 157 #if str($nmpc.nomotifprior) == 'yes':
156 --nomotifprior 'true' 158 --nomotifprior
157 --memenmotifs $nmpc.memenmotifs 159 --memenmotifs $nmpc.memenmotifs
158 --mememinw $nmpc.mememinw 160 --mememinw $nmpc.mememinw
159 --mememaxw $nmpc.mememaxw 161 --mememaxw $nmpc.mememaxw
160 #end if 162 #end if
161 #end if 163 #end if
164 ## Reporting binding events 166 ## Reporting binding events
165 #if str($rbec.report_binding_events) == 'yes': 167 #if str($rbec.report_binding_events) == 'yes':
166 --minqvalue $rbec.minqvalue 168 --minqvalue $rbec.minqvalue
167 --minfold $rbec.minfold 169 --minfold $rbec.minfold
168 #if str($rbec.nodifftests) == 'no': 170 #if str($rbec.nodifftests) == 'no':
169 --nodifftests 'true' 171 --nodifftests
170 #end if 172 #end if
171 --edgerod $rbec.edgerod 173 --edgerod $rbec.edgerod
172 --diffp $rbec.diffp 174 --diffp $rbec.diffp
173 #end if 175 #end if
174 #end if 176 #end if
175 --output_html_files_path '$output_html.files_path' 177 2>&1
176 --replicates_counts '$replicates_counts' 178 --out '$output_html.files_path'
177 --output_bed '$output_bed' 179 && mv $output_dir/*.counts '$replicates_counts'
178 --output_html '$output_html' 180 && mv $output_dir/*.bed '$output_bed'
179 --all_events_table '$all_events_table' 181 && mv $output_dir/*.html '$output_html'
182 && mv $output_dir/*.table.txt '$all_events_table'
180 ]]> 183 ]]>
181 </command> 184 </command>
182 <inputs> 185 <inputs>
183 <conditional name="single_or_multi_expt_cond"> 186 <conditional name="single_or_multi_expt_cond">
184 <param name="single_or_multi_expt" type="select" label="Run MultiGPS on single or multiple inputs?"> 187 <param name="single_or_multi_expt" type="select" label="Run MultiGPS on single or multiple inputs?">