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comparison ideas.xml @ 72:6dece3e06a10 draft

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Uploaded
author greg
date Thu, 24 Aug 2017 08:22:38 -0400
parents 4afd642aa3ce
children 11fe683a0a93
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71:4afd642aa3ce 72:6dece3e06a10
8 <requirement type="package" version="1.2.0">ideas</requirement> 8 <requirement type="package" version="1.2.0">ideas</requirement>
9 <requirement type="package" version="1.3.2">r-optparse</requirement> 9 <requirement type="package" version="1.3.2">r-optparse</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #set tmp_dir = "tmp" 12 #set tmp_dir = "tmp"
13 #set prep_input_config = "prep_input_config.txt"
13 #set prep_output_config = "prep_output_config.txt" 14 #set prep_output_config = "prep_output_config.txt"
14 ############################################## 15 ##############################################
15 ## Create the config file and prepare the data 16 ## Create the config file and prepare the data
16 ############################################## 17 ##############################################
17 #set input_type = $input_type_cond.input_type 18 #set input_type = $input_type_cond.input_type
18 #if str($input_type) == "datasets": 19 #if str($input_type) == "datasets":
19 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 20 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
20 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor 21 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
21 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 22 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
22 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 23 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
23 cp '$gen_prep_input_config' "prep_input_config.txt" && 24 cp '$gen_prep_input_config' $prep_input_config &&
24 prepMat 25 prepMat
25 '$prep_input_config' 26 $prep_input_config
26 #if str($specify_genomic_window) == 'yes': 27 #if str($specify_genomic_window) == 'yes':
27 -bed '$specify_genomic_window_cond.bed_input' 28 -bed '$specify_genomic_window_cond.bed_input'
28 #else: 29 #else:
29 -gsz '$chromInfo' 30 -gsz '$chromInfo'
30 -wsz $specify_genomic_window_cond.window_size 31 -wsz $specify_genomic_window_cond.window_size
107 && mv ./*.para $output_para 108 && mv ./*.para $output_para
108 && mv ./*.profile $output_profile 109 && mv ./*.profile $output_profile
109 && mv ./*.state $output_state 110 && mv ./*.state $output_state
110 ]]></command> 111 ]]></command>
111 <configfiles> 112 <configfiles>
112 <configfile name="prep_input_config"><![CDATA[ 113 <configfile name="gen_prep_input_config"><![CDATA[
113 #if $input_type_cond == "datasets" and $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual": 114 #if $input_type_cond == "datasets" and $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual":
114 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat: 115 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
115 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 116 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
116 #end for 117 #end for
117 #end if]]></configfile> 118 #end if]]></configfile>