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comparison ideas.xml @ 103:705c4f8fbefd draft

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Uploaded
author greg
date Tue, 14 Nov 2017 08:47:29 -0500
parents dad89ec8846f
children 4e3a891ca4d8
comparison
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102:dad89ec8846f 103:705c4f8fbefd
14 #set prep_output_config = "prep_output_config.txt" 14 #set prep_output_config = "prep_output_config.txt"
15 ############################################## 15 ##############################################
16 ## Create the config file and prepare the data 16 ## Create the config file and prepare the data
17 ############################################## 17 ##############################################
18 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 18 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
19 mkdir $output_dir &&
19 cp '$gen_prep_input_config' $prep_input_config && 20 cp '$gen_prep_input_config' $prep_input_config &&
20 prepMat 21 prepMat
21 $prep_input_config 22 $prep_input_config
22 #if str($specify_genomic_window) == "yes": 23 #if str($specify_genomic_window) == "yes":
23 -bed '$specify_genomic_window_cond.bed_input' 24 -bed '$specify_genomic_window_cond.bed_input'
89 #if str($save_ideas_log) == "yes": 90 #if str($save_ideas_log) == "yes":
90 > $output_log 91 > $output_log
91 #else: 92 #else:
92 > /dev/null 93 > /dev/null
93 #end if 94 #end if
95 && mv ./*.cluster output_dir
96 && mv ./*.para output_dir
97 && mv ./*.profile output_dir
98 && mv ./*.state output_dir
94 ]]></command> 99 ]]></command>
95 <configfiles> 100 <configfiles>
96 <configfile name="gen_prep_input_config"><![CDATA[#import os 101 <configfile name="gen_prep_input_config"><![CDATA[#import os
97 #if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 102 #if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
98 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 103 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
197 <outputs> 202 <outputs>
198 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}"> 203 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
199 <filter>save_ideas_log == 'yes'</filter> 204 <filter>save_ideas_log == 'yes'</filter>
200 </data> 205 </data>
201 <collection name="output" type="list"> 206 <collection name="output" type="list">
202 <discover_datasets pattern="__name__" format="txt"/> 207 <discover_datasets pattern="__name__" directory="output_dir" format="txt"/>
203 </collection> 208 </collection>
204 </outputs> 209 </outputs>
205 <tests> 210 <tests>
206 <test> 211 <test>
207 <param name="cell_type_epigenetic_factor" value="extract"/> 212 <param name="cell_type_epigenetic_factor" value="extract"/>