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comparison ideas.xml @ 158:c996089f1747 draft

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Uploaded
author greg
date Fri, 12 Jan 2018 14:14:19 -0500
parents b63f2ae4261a
children e4ae4106fed7
comparison
equal deleted inserted replaced
157:b63f2ae4261a 158:c996089f1747
177 --save_ideas_log $save_ideas_log 177 --save_ideas_log $save_ideas_log
178 --output_log '$output_log' 178 --output_log '$output_log'
179 #end if 179 #end if
180 #end if 180 #end if
181 #if str($perform_training) == "yes": 181 #if str($perform_training) == "yes":
182 #set heatmaps_input_dir = $output_training_dir
183 && mv ./*.para0 '$output_training_dir' 182 && mv ./*.para0 '$output_training_dir'
184 && mv ./*.profile0 '$output_training_dir' 183 && mv ./*.profile0 '$output_training_dir'
184 #if str($output_heatmaps) == "yes":
185 && Rscript '$__tool_directory__/create_heatmaps.R'
186 --input_dir 'input_training_dir'
187 --output_dir '$output_pdf_dir'
188 --script_dir '$__tool_directory__'
189 --training_mode true
190 #end if
191 #end if
185 #else: 192 #else:
186 #set heatmaps_input_dir = $output_txt_dir
187 && mv ./*.cluster '$output_txt_dir' 193 && mv ./*.cluster '$output_txt_dir'
188 && mv ./*.para '$output_txt_dir' 194 && mv ./*.para '$output_txt_dir'
189 && mv ./*.profile '$output_txt_dir' 195 && mv ./*.profile '$output_txt_dir'
190 && mv ./*.state '$output_txt_dir' 196 && mv ./*.state '$output_txt_dir'
191 #end if 197 #if str($output_heatmaps) == "yes":
192 #if str($output_heatmaps) == "yes": 198 && Rscript '$__tool_directory__/create_heatmaps.R'
193 && Rscript '$__tool_directory__/create_heatmaps.R' 199 --input_dir '$output_txt_dir'
194 --input_dir '$heatmaps_input_dir' 200 --output_dir '$output_pdf_dir'
195 --output_dir '$output_pdf_dir' 201 --script_dir '$__tool_directory__'
196 --script_dir '$__tool_directory__' 202 #end if
197 #end if 203 #end if
198 ]]></command> 204 ]]></command>
199 <configfiles> 205 <configfiles>
200 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 206 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
201 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 207 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions