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comparison multigps.xml @ 27:968f95d4d13e draft

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author iuc
date Wed, 05 Apr 2017 10:06:47 -0400
parents 0c48a4ed47a0
children c290150f83f9
comparison
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26:0c48a4ed47a0 27:968f95d4d13e
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 #set output_dir = $output_html.files_path 11 #set output_dir = $output_html.files_path
12 mkdir -p $output_dir && 12 mkdir -p $output_dir &&
13 python '$build_design_file' '$inputs' &&
14 multigps 13 multigps
15 ## General options 14 ## General options
16 --design 'design.tabular' 15 --design '$build_design_file'
17 ## Append .txt extensions to events hrefs 16 ## Append .txt extensions to events hrefs
18 ## in output dataset so files will render 17 ## in output dataset so files will render
19 ## in the browser. 18 ## in the browser.
20 --eventsaretxt 19 --eventsaretxt
21 ## Do not run the parallel version of meme. 20 ## Do not run the parallel version of meme.
152 && mv $output_dir/*.html '$output_html' 151 && mv $output_dir/*.html '$output_html'
153 && mv $output_dir/*.table.txt '$all_events_table' 152 && mv $output_dir/*.table.txt '$all_events_table'
154 ]]> 153 ]]>
155 </command> 154 </command>
156 <configfiles> 155 <configfiles>
157 <inputs name="inputs"/>
158 <configfile name="build_design_file"> 156 <configfile name="build_design_file">
159 <![CDATA[ 157 <![CDATA[
160 import json 158 #for $condition_items in $condition_repeat:
161 import sys 159 #for $signal_items in $condition_items.signal_repeat:
162 160 #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
163 inputs_path = sys.argv[1] 161 #set $frc = $signal_items.fixedreadcount_cond.fixedreadcount
164 params = json.load(open(inputs_path, 'r')) 162 #else
165 condition_repeat = params['condition_repeat'] 163 #set $frc = ''
166 fh = open('design.tabular', 'w') 164 #end if
167 fh.write('%s\n' % str(params)) 165 ${signal_items.signal} Signal ${signal_items.signal.ext.upper()} ${signal_items.condition_name} ${signal_items.replicate_name} ${signal_items.experiment_type} ${frc}
168 for condition_items in condition_repeat: 166 #end for
169 for signal_items in condition_items['signal_repeat']: 167 #for $control_items in $condition_items.control_repeat:
170 signal = signal_items['signal'] 168 #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes':
171 condition_name = signal_items['condition_name'] 169 #set $rn = $control_items.specify_replicate_name_cond.replicate_name
172 replicate_name = signal_items['replicate_name'] 170 #else:
173 experiment_type = signal['experiment_type'] 171 #set $rn = ''
174 line_items = [signal.file_name, 'Signal', signal.ext.upper(), condition_name, replicate_name, experiment_type] 172 #end if
175 fixedreadcount_cond = signal_items['fixedreadcount_cond'] 173 #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
176 fixedreadcount_select = fixedreadcount_cond['fixedreadcount_select'] 174 #set $frc = $control_items.fixedreadcount_cond.fixedreadcount
177 if fixedreadcount_select == 'yes': 175 #else:
178 line_items.append(fixedreadcount_cond['fixedreadcount']) 176 #set $frc = ''
179 fh.write('%s\n' % '\t'.join(line_items)) 177 #end if
180 for control_items in condition_items['control_repeat']: 178 ${control_items.control} Control ${control_items.control.ext.upper()} ${control_items.condition_name} ${rn} ${control_items.experiment_type} ${frc}
181 control = control_items['control'] 179 #end for
182 experiment_type = control_items['experiment_type'] 180 #end for
183 condition_name = control_items['condition_name']
184 line_items = [control.file_name, 'Control', control.ext.upper(), condition_name]
185 specify_replicate_name_cond = control_items['specify_replicate_name_cond']
186 specify_replicate_name = specify_replicate_name_cond['specify_replicate_name']
187 if specify_replicate_name == 'yes':
188 line_items.append(specify_replicate_name_cond['replicate_name'])
189 line_items.append(experiment_type)
190 fixedreadcount_cond = control_items['fixedreadcount_cond']
191 fixedreadcount_select = fixedreadcount_cond['fixedreadcount_select']
192 if fixedreadcount_select == 'yes':
193 line_items.append(fixedreadcount_cond['fixedreadcount'])
194 fh.write('%s\n' % '\t'.join(line_items))
195 fh.close()
196 ]]> 181 ]]>
197 </configfile> 182 </configfile>
198 </configfiles> 183 </configfiles>
199 <inputs> 184 <inputs>
200 <repeat name="condition_repeat" title="Condition" min="1"> 185 <repeat name="condition_repeat" title="Condition" min="1">