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comparison ideas.xml @ 67:0f186cb552c8 draft

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Uploaded
author greg
date Thu, 24 Aug 2017 08:05:46 -0400
parents dc5d5a08c370
children 5fb237a06499
comparison
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66:dc5d5a08c370 67:0f186cb552c8
13 #set prep_output_config = "prep_output_config.txt" 13 #set prep_output_config = "prep_output_config.txt"
14 ############################################## 14 ##############################################
15 ## Create the config file and prepare the data 15 ## Create the config file and prepare the data
16 ############################################## 16 ##############################################
17 #set input_type = $input_type_cond.input_type 17 #set input_type = $input_type_cond.input_type
18 cp '$prep_input_config' 'prep_input_config.txt' && 18 #if str($input_type) == "datasets":
19 prepMat 19 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
20 #if str($input_type) == 'datasets': 20 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
21 '$prep_input_config'
22 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 21 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
23 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 22 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
23 cp '$gen_prep_input_config' "prep_input_config.txt" &&
24 prepMat
25 '$prep_input_config'
24 #if str($specify_genomic_window) == 'yes': 26 #if str($specify_genomic_window) == 'yes':
25 -bed '$specify_genomic_window_cond.bed_input' 27 -bed '$specify_genomic_window_cond.bed_input'
26 #else: 28 #else:
27 -gsz '$chromInfo' 29 -gsz '$chromInfo'
28 -wsz $specify_genomic_window_cond.window_size 30 -wsz $specify_genomic_window_cond.window_size