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comparison multigps.xml @ 35:150859e7f99b draft

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Uploaded
author greg
date Wed, 14 Dec 2016 09:24:00 -0500
parents 9b48edaa54f8
children 8fca5f834b15
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34:9b48edaa54f8 35:150859e7f99b
25 ############################ 25 ############################
26 ## Advanced options 26 ## Advanced options
27 ############################ 27 ############################
28 #set aoc = $advanced_options_cond 28 #set aoc = $advanced_options_cond
29 #if str($aoc.advanced_options) == 'display': 29 #if str($aoc.advanced_options) == 'display':
30 #set bmsc = $aoc.binding_model_smoothing_cond
30 #set gmsc = $aoc.gauss_model_smoothing_cond 31 #set gmsc = $aoc.gauss_model_smoothing_cond
31 #set rbec = $aoc.report_binding_events_cond 32 #set rbec = $aoc.report_binding_events_cond
32 #set rloc = $aoc.reads_limits_options_cond 33 #set rloc = $aoc.reads_limits_options_cond
33 #set sdc = $aoc.scale_data_cond 34 #set sdc = $aoc.scale_data_cond
34 #set umc = $aoc.use_motif_cond 35 #set umc = $aoc.use_motif_cond
91 ############################ 92 ############################
92 #if str($aoc.nomodelupdate) == 'no': 93 #if str($aoc.nomodelupdate) == 'no':
93 --nomodelupdate 94 --nomodelupdate
94 #end if 95 #end if
95 --minmodelupdateevents $aoc.minmodelupdateevents 96 --minmodelupdateevents $aoc.minmodelupdateevents
96 #if str($aoc.nomodelsmoothing) == 'no': 97 #if str($bmsc.nomodelsmoothing) == 'no':
97 --nomodelsmoothing 98 --nomodelsmoothing
98 #end if 99 #else:
99 --splinesmoothparam $aoc.splinesmoothparam 100 --splinesmoothparam $bmsc.splinesmoothparam
101 #end if
100 #if str($gmsc.gaussmodelsmoothing) == 'yes': 102 #if str($gmsc.gaussmodelsmoothing) == 'yes':
101 --gaussmodelsmoothing 103 --gaussmodelsmoothing
102 --gausssmoothparam $gmsc.gausssmoothparam 104 --gausssmoothparam $gmsc.gausssmoothparam
103 #end if 105 #end if
104 #if str($aoc.jointinmodel) == 'yes': 106 #if str($aoc.jointinmodel) == 'yes':
249 <param name="nomodelupdate" type="select" label="Perform binding model updates?"> 251 <param name="nomodelupdate" type="select" label="Perform binding model updates?">
250 <option value="yes" selected="True">Yes</option> 252 <option value="yes" selected="True">Yes</option>
251 <option value="no">No</option> 253 <option value="no">No</option>
252 </param> 254 </param>
253 <param name="minmodelupdateevents" type="integer" value="500" min="0" label="Minimum number of events to support an update of the read distribution" /> 255 <param name="minmodelupdateevents" type="integer" value="500" min="0" label="Minimum number of events to support an update of the read distribution" />
254 <param name="nomodelsmoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline."> 256 <conditional name="binding_model_smoothing_cond">
255 <option value="yes" selected="True">Yes</option> 257 <param name="nomodelsmoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline.">
256 <option value="no">No</option> 258 <option value="yes" selected="True">Yes</option>
257 </param> 259 <option value="no">No</option>
258 <param name="splinesmoothparam" type="integer" value="30" min="0" label="Spline smoothing parameter" /> 260 </param>
261 <when value="yes">
262 <param name="splinesmoothparam" type="integer" value="30" min="0" label="Spline smoothing parameter" />
263 </when>
264 <when value="no" />
265 </conditional>
259 <conditional name="gauss_model_smoothing_cond"> 266 <conditional name="gauss_model_smoothing_cond">
260 <param name="gaussmodelsmoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline."> 267 <param name="gaussmodelsmoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline.">
261 <option value="no" selected="True">No</option> 268 <option value="no" selected="True">No</option>
262 <option value="yes">Yes</option> 269 <option value="yes">Yes</option>
263 </param> 270 </param>