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comparison ideas.xml @ 153:1dc3ef0a6312 draft

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Uploaded
author greg
date Fri, 12 Jan 2018 13:43:08 -0500
parents 9d34f7e6d80c
children f70a86b6c6e0
comparison
equal deleted inserted replaced
152:26c26cb32137 153:1dc3ef0a6312
10 <requirement type="package" version="1.4.4">r-optparse</requirement> 10 <requirement type="package" version="1.4.4">r-optparse</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #set output_pdf_dir = "output_pdf_dir" 13 #set output_pdf_dir = "output_pdf_dir"
14 #set output_txt_dir = "output_txt_dir" 14 #set output_txt_dir = "output_txt_dir"
15 #set output_txt_dir = "output_training_dir"
15 #set tmp_dir = "tmp" 16 #set tmp_dir = "tmp"
16 #set prep_input_config = "prep_input_config.txt" 17 #set prep_input_config = "prep_input_config.txt"
17 #set prep_output_config = "prep_output_config.txt" 18 #set prep_output_config = "prep_output_config.txt"
18 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
19 #set perform_training = $perform_training_cond.perform_training 20 #set perform_training = $perform_training_cond.perform_training
20 ############################################## 21 ##############################################
21 ## Create the config file and prepare the data 22 ## Create the config file and prepare the data
22 ############################################## 23 ##############################################
23 #if str($output_heatmaps) == "yes": 24 #if str($output_heatmaps) == "yes":
24 mkdir '$output_pdf_dir' && 25 mkdir '$output_pdf_dir' &&
26 #end if
27 #if str($perform_training) == "yes":
28 mkdir '$output_training_dir' &&
25 #end if 29 #end if
26 mkdir '$output_txt_dir' && 30 mkdir '$output_txt_dir' &&
27 cp '$gen_prep_input_config' $prep_input_config && 31 cp '$gen_prep_input_config' $prep_input_config &&
28 sort $prep_input_config -o $prep_input_config && 32 sort $prep_input_config -o $prep_input_config &&
29 prepMat 33 prepMat
172 #if str($save_ideas_log) == "yes": 176 #if str($save_ideas_log) == "yes":
173 --save_ideas_log $save_ideas_log 177 --save_ideas_log $save_ideas_log
174 --output_log '$output_log' 178 --output_log '$output_log'
175 #end if 179 #end if
176 #end if 180 #end if
177 && mv ./*.cluster '$output_txt_dir' 181 #if str($perform_training) == "yes":
178 && mv ./*.para '$output_txt_dir' 182 && mv ./*.para0 '$output_training_dir'
179 && mv ./*.profile '$output_txt_dir' 183 && mv ./*.profile0 '$output_training_dir'
180 && mv ./*.state '$output_txt_dir' 184 #else:
185 && mv ./*.cluster '$output_txt_dir'
186 && mv ./*.para '$output_txt_dir'
187 && mv ./*.profile '$output_txt_dir'
188 && mv ./*.state '$output_txt_dir'
189 #end if
181 #if str($output_heatmaps) == "yes": 190 #if str($output_heatmaps) == "yes":
182 && Rscript '$__tool_directory__/create_heatmaps.R' 191 && Rscript '$__tool_directory__/create_heatmaps.R'
183 --input_dir '$output_txt_dir' 192 --input_dir '$output_txt_dir'
184 --output_dir '$output_pdf_dir' 193 --output_dir '$output_pdf_dir'
185 --script_dir '$__tool_directory__' 194 --script_dir '$__tool_directory__'
215 <param name="perform_training" type="select" label="Perform training?"> 224 <param name="perform_training" type="select" label="Perform training?">
216 <option value="yes" selected="true">Yes</option> 225 <option value="yes" selected="true">Yes</option>
217 <option value="no">No</option> 226 <option value="no">No</option>
218 </param> 227 </param>
219 <when value="yes"> 228 <when value="yes">
220 <param name="training_iterations" type="integer" value="20" min="1" label="Number of training iterations"/> 229 <param name="training_iterations" type="integer" value="20" min="2" label="Number of training iterations"/>
221 <param name="training_windows" type="integer" value="10000" min="1" label="Number of randomly selected windows for training"/> 230 <param name="training_windows" type="integer" value="10000" min="2" label="Number of randomly selected windows for training"/>
222 </when> 231 </when>
223 <when value="no"/> 232 <when value="no"/>
224 </conditional> 233 </conditional>
225 <conditional name="cell_type_epigenetic_factor_cond"> 234 <conditional name="cell_type_epigenetic_factor_cond">
226 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by"> 235 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
315 <discover_datasets pattern="__name__" directory="output_pdf_dir" format="pdf"/> 324 <discover_datasets pattern="__name__" directory="output_pdf_dir" format="pdf"/>
316 <filter>output_heatmaps == 'yes'</filter> 325 <filter>output_heatmaps == 'yes'</filter>
317 </collection> 326 </collection>
318 <collection name="output_txt_collection" type="list"> 327 <collection name="output_txt_collection" type="list">
319 <discover_datasets pattern="__name__" directory="output_txt_dir" format="txt"/> 328 <discover_datasets pattern="__name__" directory="output_txt_dir" format="txt"/>
329 <filter>perform_training_cond['perform_training'] == 'no'</filter>
330 </collection>
331 <collection name="output_ttraining_collection" type="list">
332 <discover_datasets pattern="__name__" directory="output_training_dir" format="txt"/>
333 <filter>perform_training_cond['perform_training'] == 'yes'</filter>
320 </collection> 334 </collection>
321 </outputs> 335 </outputs>
322 <tests> 336 <tests>
323 <test> 337 <test>
324 <param name="cell_type_epigenetic_factor" value="extract"/> 338 <param name="cell_type_epigenetic_factor" value="extract"/>