Mercurial > repos > greg > multigps
comparison multigps.xml @ 35:150859e7f99b draft
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> |