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comparison multigps.xml @ 7:6d6ceda98d94 draft

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author iuc
date Tue, 04 Apr 2017 14:40:36 -0400
parents 7dc47046b54c
children 2e5d3c304171
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6:7dc47046b54c 7:6d6ceda98d94
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 $output_dir &&
13 python '$design_file_script' '$inputs' && 13 '$design_file' &&
14 multigps 14 multigps
15 ## General options 15 ## General options
16 #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt
17 #if str($single_or_multi_expt) == 'multi':
18 #for $i in $single_or_multi_expt_cond['input_items']:
19 #set label_cond = $i['label_cond']
20 #set experiment_file_name = $label_cond.input
21 #set label = $label_cond.label
22 #set file_format = $label_cond.input.ext
23 #set control_file_name = $label_cond.control
24 #set condition_name = $label_cond.condition_name
25 #set replicate_name = 'None'
26 #set experiment_type = $label_cond.experiment_type
27 #set fixed_read_count = $label_cond.fixedreadcount
28 #if str($label) == 'Signal':
29 #set replicate_name = $label_cond.replicate_name
30 #else if str($label) == 'Control':
31 #set rncond = $label_cond.replicate_name_cond
32 #if str($rncond.specify_replicate_name) == 'yes':
33 #set replicate_name = $rncond.replicate_name
34 #end if
35 #end if
36 --input_item '$experiment_file_name' '$control_file_name' '$label' '$file_format' '$condition_name' '$replicate_name' '$experiment_type' '$fixed_read_count'
37 #end for
38 #else:
39 #set expt = $single_or_multi_expt_cond.expt
40 #set control = $single_or_multi_expt_cond.control
41 --expt '$expt'
42 --format $expt.ext
43 #if str($control) != 'None':
44 --control '$control'
45 #end if
46 #end if
47 ## Append .txt extensions to events hrefs 16 ## Append .txt extensions to events hrefs
48 ## in output dataset so files will render 17 ## in output dataset so files will render
49 ## in the browser. 18 ## in the browser.
50 --eventsaretxt 19 --eventsaretxt
51 ## Do not run the parallel version of meme. 20 ## Do not run the parallel version of meme.
183 && mv $output_dir/*.table.txt '$all_events_table' 152 && mv $output_dir/*.table.txt '$all_events_table'
184 ]]> 153 ]]>
185 </command> 154 </command>
186 <configfiles> 155 <configfiles>
187 <inputs name="inputs"/> 156 <inputs name="inputs"/>
188 <configfile name="design_file_script"> 157 <configfile name="design_file">
189 <![CDATA[ 158 <![CDATA[
190 import sys 159 #for cond_i, condition_items in enumerate($condition_repeat):
191 import json 160 #for experiment_items in condition_items['experiment_repeat']:
192 161 #set experiment = $experiment_items['experiment']
193 input_json_path = sys.argv[1] 162 #set replicate_name = $experiment_items['replicate_name']
194 params = json.load(open(input_json_path, "r")) 163 #set experiment_type = $experiment_items['experiment_type']
195 164 #set line = str($experiment) + 'Signal' + str($experiment.ext.upper()) + str($cond_i) + str($replicate_name) + str($experiment_type)
196 if params['single_or_multi_expt_cond']['single_or_multi_expt'] == 'multi': 165 #set fixedreadcount_cond = $experiment_items['fixedreadcount_cond']
197 input_items = params['single_or_multi_expt_cond']['input_items'] 166 #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
198 design_file = open('design.tabular', 'w') 167 #if str($fixedreadcount_select) == 'yes':
199 for item in input_items: 168 #set $line += str($fixedreadcount_cond['fixedreadcount'])
200 experiment_file_name, control_file_name, label, file_format, condition_name, replicate_name, experiment_type, fixed_read_count = item 169 #end if
201 if control_file_name not in ['None', None, '']: 170 '%s\n' % $line
202 control_file_names.append(control_file_name) 171 #end for
203 file_format = file_format.upper() 172 #for control_items in condition_items['control_repeat']:
204 items = [experiment_file_name, label, file_format, condition_name] 173 #set control = $control_items['control']
205 if replicate_name not in ['None', None, '']: 174 #set experiment_type = $control_items['experiment_type']
206 items.append(replicate_name) 175 #set line = str($control_items) + 'Control' + str($control.ext.upper()) + str($cond_i)
207 if experiment_type not in ['None', None, '']: 176 #set specify_replicate_name_cond = $control_items['specify_replicate_name_cond']
208 items.append(experiment_type) 177 #set specify_replicate_name = $specify_replicate_name_cond.specify_replicate_name
209 if fixed_read_count not in ['None', None, '']: 178 #if str($specify_replicate_name) == 'yes':
210 items.append(fixed_read_count) 179 #set $line += str($specify_replicate_name_cond['replicate_name'])
211 design_file.write('%s\n' % '\t'.join(items)) 180 #end if
212 design_file.close() 181 #set $line += str($experiment_type)
182 #set fixedreadcount_cond = $experiment_items['fixedreadcount_cond']
183 #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
184 #if str($fixedreadcount_select) == 'yes':
185 #set $line += str($fixedreadcount_cond['fixedreadcount'])
186 #end if
187 '%s\n' % $line
188 #end for
189 #end for
213 ]]> 190 ]]>
214 </configfile> 191 </configfile>
215 </configfiles> 192 </configfiles>
216 <inputs> 193 <inputs>
217 <conditional name="single_or_multi_expt_cond"> 194 <repeat name="condition_repeat" title="Condition" min="1">
218 <param name="single_or_multi_expt" type="select" label="Run MultiGPS on single or multiple inputs?"> 195 <repeat name="experiment_repeat" title="Experiment" min="1">
219 <option value="multi" selected="True">Multiple inputs</option> 196 <param name="experiment" type="data" format="bam,bed,scidx" label="Select experiment" help="Supported formats are bam, bed and scidx">
220 <option value="single">Single input</option>
221 </param>
222 <when value="multi">
223 <repeat name="input_items" title="Input files, attributes and options" min="2">
224 <conditional name="label_cond">
225 <param name="label" type="select" label="This experiment is">
226 <option value="Signal" selected="True">Signal</option>
227 <option value="Control">Control</option>
228 </param>
229 <when value="Signal">
230 <expand macro="label_cond_params_start" />
231 <param name="replicate_name" type="text" label="Replicate name" />
232 <expand macro="label_cond_params_end" />
233 </when>
234 <when value="Control">
235 <expand macro="label_cond_params_start" />
236 <conditional name="replicate_name_cond">
237 <param name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control experiments. If used, the control will only be used for the corresponding named signal replicate">
238 <option value="no" selected="True">No</option>
239 <option value="yes">Yes</option>
240 </param>
241 <when value="yes">
242 <param name="replicate_name" type="text" optional="True" label="Replicate name"/>
243 </when>
244 <when value="no" />
245 </conditional>
246 <expand macro="label_cond_params_end" />
247 </when>
248 </conditional>
249 </repeat>
250 </when>
251 <when value="single">
252 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
253 <validator type="unspecified_build" /> 197 <validator type="unspecified_build" />
254 </param> 198 </param>
255 <param name="control" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" /> 199 <expand macro="param_experiment_type" />
256 </when> 200 <param name="replicate_name" type="text" label="Replicate name" />
257 </conditional> 201 <expand macro="cond_fixedreadcount" />
202 </repeat>
203 <repeat name="control_repeat" title="Control" min="0">
204 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
205 <validator type="unspecified_build" />
206 </param>
207 <expand macro="param_experiment_type" />
208 <conditional name="specify_replicate_name_cond">
209 <param name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control experiments. If used, the control will only be used for the corresponding named signal replicate">
210 <option value="no" selected="True">No</option>
211 <option value="yes">Yes</option>
212 </param>
213 <when value="yes">
214 <param name="replicate_name" type="text" optional="True" label="Replicate name"/>
215 </when>
216 <when value="no" />
217 </conditional>
218 <expand macro="cond_fixedreadcount" />
219 </repeat>
220 </repeat>
258 <!-- Advanced options --> 221 <!-- Advanced options -->
259 <conditional name="advanced_options_cond"> 222 <conditional name="advanced_options_cond">
260 <param name="advanced_options" type="select" label="Advanced options"> 223 <param name="advanced_options" type="select" label="Advanced options">
261 <option value="hide" selected="true">Hide</option> 224 <option value="hide" selected="true">Hide</option>
262 <option value="display">Display</option> 225 <option value="display">Display</option>