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comparison multigps.xml @ 24:d5c1ab05259b draft

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Uploaded
author greg
date Wed, 14 Dec 2016 07:45:02 -0500
parents ffefb407c22a
children 32a59270224b
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23:ffefb407c22a 24:d5c1ab05259b
12 ############################ 12 ############################
13 ## General options 13 ## General options
14 ############################ 14 ############################
15 --expt "$expt" 15 --expt "$expt"
16 --format "$expt.ext" 16 --format "$expt.ext"
17 #if len($ctrl) > 0: 17 #if $ctrl is not None:
18 --ctrl "$ctrl" 18 --ctrl "$ctrl"
19 #end if 19 #end if
20 #if str($verbose) == 'yes': 20 #if str($verbose) == 'yes':
21 --verbose 21 --verbose
22 #end if 22 #end if
23 --threads="\${GALAXY_SLOTS:-4}" 23 --threads="\${GALAXY_SLOTS:-4}"
24 ############################ 24 ############################
25 ## Advanced options 25 ## Advanced options
26 ############################ 26 ############################
27 #set aoc = $advanced_options_cond 27 #set aoc = $advanced_options_cond
28 #set bmsc = $aoc.binding_model_smoothing_cond
29 #set gmsc = $aoc.gauss_model_smoothing_cond 28 #set gmsc = $aoc.gauss_model_smoothing_cond
30 #set rbec = $aoc.report_binding_events_cond 29 #set rbec = $aoc.report_binding_events_cond
31 #set rloc = $aoc.reads_limits_options_cond 30 #set rloc = $aoc.reads_limits_options_cond
32 #set sdc = $aoc.scale_data_cond 31 #set sdc = $aoc.scale_data_cond
33 #set umc = $aoc.use_motif_cond 32 #set umc = $aoc.use_motif_cond
79 ############################ 78 ############################
80 #if str($aoc.nomodelupdate) == 'no': 79 #if str($aoc.nomodelupdate) == 'no':
81 --nomodelupdate 80 --nomodelupdate
82 #end if 81 #end if
83 --minmodelupdateevents $aoc.minmodelupdateevents 82 --minmodelupdateevents $aoc.minmodelupdateevents
84 #if str($bmsc.nomodelsmoothing) == 'no': 83 #if str($aoc.nomodelsmoothing) == 'no':
85 --nomodelsmoothing 84 --nomodelsmoothing
86 #end if 85 #end if
87 --splinesmoothparam $aoc.splinesmoothparam 86 --splinesmoothparam $aoc.splinesmoothparam
88 #if str($gmsc.gaussmodelsmoothing) == 'yes': 87 #if str($gmsc.gaussmodelsmoothing) == 'yes':
89 --gaussmodelsmoothing 88 --gaussmodelsmoothing