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comparison ideas.xml @ 110:aa626c85e6d3 draft

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Uploaded
author greg
date Wed, 15 Nov 2017 07:47:41 -0500
parents c47a3c6a01bd
children 0c9cdefe4b45
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109:c47a3c6a01bd 110:aa626c85e6d3
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 = '$project_name' 15 #set prep_output_config = "IDEASoutput"
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' &&
152 <validator type="unspecified_build"/> 152 <validator type="unspecified_build"/>
153 </param> 153 </param>
154 </repeat> 154 </repeat>
155 </when> 155 </when>
156 </conditional> 156 </conditional>
157 <param name="project_name" type="text" value="myProject" optional="false" label="Project name" help="Output datasets will have this base name">
158 <validator type="empty_field"/>
159 </param>
160 <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/> 157 <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/>
161 <conditional name="specify_genomic_window_cond"> 158 <conditional name="specify_genomic_window_cond">
162 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data"> 159 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
163 <option value="no" selected="true">No</option> 160 <option value="no" selected="true">No</option>
164 <option value="yes">Yes</option> 161 <option value="yes">Yes</option>