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comparison ideas.xml @ 116:e1b21d7e266a draft

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Uploaded
author greg
date Fri, 17 Nov 2017 10:03:03 -0500
parents 242ff1426fb4
children 42481a73f73d
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115:242ff1426fb4 116:e1b21d7e266a
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #set output_dir = "output_dir" 12 #set output_dir = "output_dir"
13 #set tmp_dir = "tmp" 13 #set tmp_dir = "tmp"
14 #set prep_input_config = "prep_input_config.txt" 14 #set prep_input_config = "prep_input_config.txt"
15 #set prep_output_config = "IDEAS_out" 15 #set prep_output_config = '$project_name'
16 ############################################## 16 ##############################################
17 ## Create the config file and prepare the data 17 ## Create the config file and prepare the data
18 ############################################## 18 ##############################################
19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
20 mkdir '$output_dir' && 20 mkdir '$output_dir' &&
97 && mv ./*.cluster '$output_dir' 97 && mv ./*.cluster '$output_dir'
98 && mv ./*.para '$output_dir' 98 && mv ./*.para '$output_dir'
99 && mv ./*.profile '$output_dir' 99 && mv ./*.profile '$output_dir'
100 && mv ./*.state '$output_dir' 100 && mv ./*.state '$output_dir'
101 && Rscript '$__tool_directory__/create_heatmap.R' 101 && Rscript '$__tool_directory__/create_heatmap.R'
102 -i '$output_dir/prep_output_config.txt.para' 102 -i '$output_dir/$project_name.para'
103 -o '$output_heatmap' 103 -o '$output_heatmap'
104 ]]></command> 104 ]]></command>
105 <configfiles> 105 <configfiles>
106 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 106 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
107 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 107 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions