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comparison multigps.xml @ 9:2e5d3c304171 draft

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author iuc
date Tue, 04 Apr 2017 15:17:46 -0400
parents 6d6ceda98d94
children bfe2da7083b7
comparison
equal deleted inserted replaced
8:7856ef41f093 9:2e5d3c304171
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 $output_dir &&
13 '$design_file' &&
14 multigps 13 multigps
15 ## General options 14 ## General options
15 --design '$design_file'
16 ## Append .txt extensions to events hrefs 16 ## Append .txt extensions to events hrefs
17 ## in output dataset so files will render 17 ## in output dataset so files will render
18 ## in the browser. 18 ## in the browser.
19 --eventsaretxt 19 --eventsaretxt
20 ## Do not run the parallel version of meme. 20 ## Do not run the parallel version of meme.
155 <configfiles> 155 <configfiles>
156 <inputs name="inputs"/> 156 <inputs name="inputs"/>
157 <configfile name="design_file"> 157 <configfile name="design_file">
158 <![CDATA[ 158 <![CDATA[
159 #for cond_i, condition_items in enumerate($condition_repeat): 159 #for cond_i, condition_items in enumerate($condition_repeat):
160 #for experiment_items in condition_items['experiment_repeat']: 160 #for signal_items in condition_items['signal_repeat']:
161 #set experiment = $experiment_items['experiment'] 161 #set signal = $signal_items['signal']
162 #set replicate_name = $experiment_items['replicate_name'] 162 #set replicate_name = $signal_items['replicate_name']
163 #set experiment_type = $experiment_items['experiment_type'] 163 #set experiment_type = $signal['experiment_type']
164 #set line = str($experiment) + 'Signal' + str($experiment.ext.upper()) + str($cond_i) + str($replicate_name) + str($experiment_type) 164 #set line = str($signal) + '\t' + 'Signal' + '\t' + str($signal.ext.upper()) + '\t' + str($cond_i) + '\t' + str($replicate_name) + '\t' + str($experiment_type)
165 #set fixedreadcount_cond = $experiment_items['fixedreadcount_cond'] 165 #set fixedreadcount_cond = $signal_items['fixedreadcount_cond']
166 #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select'] 166 #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
167 #if str($fixedreadcount_select) == 'yes': 167 #if str($fixedreadcount_select) == 'yes':
168 #set $line += str($fixedreadcount_cond['fixedreadcount']) 168 #set $line += + '\t' + str($fixedreadcount_cond['fixedreadcount'])
169 #end if 169 #end if
170 '%s\n' % $line 170 '%s\n' % $line
171 #end for 171 #end for
172 #for control_items in condition_items['control_repeat']: 172 #for control_items in condition_items['control_repeat']:
173 #set control = $control_items['control'] 173 #set control = $control_items['control']
174 #set experiment_type = $control_items['experiment_type'] 174 #set experiment_type = $control_items['experiment_type']
175 #set line = str($control_items) + 'Control' + str($control.ext.upper()) + str($cond_i) 175 #set line = str($control_items) + '\t' + 'Control' + '\t' + str($control.ext.upper()) + '\t' + str($cond_i)
176 #set specify_replicate_name_cond = $control_items['specify_replicate_name_cond'] 176 #set specify_replicate_name_cond = $control_items['specify_replicate_name_cond']
177 #set specify_replicate_name = $specify_replicate_name_cond.specify_replicate_name 177 #set specify_replicate_name = $specify_replicate_name_cond.specify_replicate_name
178 #if str($specify_replicate_name) == 'yes': 178 #if str($specify_replicate_name) == 'yes':
179 #set $line += str($specify_replicate_name_cond['replicate_name']) 179 #set $line += '\t' + str($specify_replicate_name_cond['replicate_name'])
180 #end if 180 #end if
181 #set $line += str($experiment_type) 181 #set $line += '\t' + str($experiment_type)
182 #set fixedreadcount_cond = $experiment_items['fixedreadcount_cond'] 182 #set fixedreadcount_cond = $control_items['fixedreadcount_cond']
183 #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select'] 183 #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
184 #if str($fixedreadcount_select) == 'yes': 184 #if str($fixedreadcount_select) == 'yes':
185 #set $line += str($fixedreadcount_cond['fixedreadcount']) 185 #set $line += '\t' + str($fixedreadcount_cond['fixedreadcount'])
186 #end if 186 #end if
187 '%s\n' % $line 187 '%s\n' % $line
188 #end for 188 #end for
189 #end for 189 #end for
190 ]]> 190 ]]>
191 </configfile> 191 </configfile>
192 </configfiles> 192 </configfiles>
193 <inputs> 193 <inputs>
194 <repeat name="condition_repeat" title="Condition" min="1"> 194 <repeat name="condition_repeat" title="Condition" min="1">
195 <repeat name="experiment_repeat" title="Experiment" min="1"> 195 <repeat name="signal_repeat" title="Signal" min="1">
196 <param name="experiment" type="data" format="bam,bed,scidx" label="Select experiment" help="Supported formats are bam, bed and scidx"> 196 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
197 <validator type="unspecified_build" /> 197 <validator type="unspecified_build" />
198 </param> 198 </param>
199 <expand macro="param_experiment_type" /> 199 <expand macro="param_experiment_type" />
200 <param name="replicate_name" type="text" label="Replicate name" /> 200 <param name="replicate_name" type="text" label="Replicate name" />
201 <expand macro="cond_fixedreadcount" /> 201 <expand macro="cond_fixedreadcount" />
204 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx"> 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" /> 205 <validator type="unspecified_build" />
206 </param> 206 </param>
207 <expand macro="param_experiment_type" /> 207 <expand macro="param_experiment_type" />
208 <conditional name="specify_replicate_name_cond"> 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"> 209 <param name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control. If used, the control will only be used for the corresponding named signal replicate">
210 <option value="no" selected="True">No</option> 210 <option value="no" selected="True">No</option>
211 <option value="yes">Yes</option> 211 <option value="yes">Yes</option>
212 </param> 212 </param>
213 <when value="yes"> 213 <when value="yes">
214 <param name="replicate_name" type="text" optional="True" label="Replicate name"/> 214 <param name="replicate_name" type="text" optional="True" label="Replicate name"/>
246 </param> 246 </param>
247 </when> 247 </when>
248 </conditional> 248 </conditional>
249 <!-- Scaling data --> 249 <!-- Scaling data -->
250 <conditional name="scale_data_cond"> 250 <conditional name="scale_data_cond">
251 <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using regression on the set of signal/control ratios in 10Kbp windows."> 251 <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method described by Liang & Ketes, BMC Bioinformatics 2012.">
252 <option value="no" selected="True">No</option> 252 <option value="no" selected="True">No</option>
253 <option value="yes">Yes</option> 253 <option value="yes">Yes</option>
254 </param> 254 </param>
255 <when value="yes"> 255 <when value="yes">
256 <param name="scaling" type="select" label="Use signal vs control scaling?"> 256 <param name="scaling" type="select" label="Use signal vs control scaling?">