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comparison multigps.xml @ 40:9d4d90d4458a draft

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author iuc
date Thu, 06 Apr 2017 09:32:38 -0400
parents befabf136da4
children d08ca1690fa1
comparison
equal deleted inserted replaced
39:ca90b0b3bd64 40:9d4d90d4458a
158 #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes': 158 #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
159 #set $frc = $signal_items.fixedreadcount_cond.fixedreadcount 159 #set $frc = $signal_items.fixedreadcount_cond.fixedreadcount
160 #else: 160 #else:
161 #set $frc = '' 161 #set $frc = ''
162 #end if 162 #end if
163 ${signal_items.signal} Signal ${signal_items.signal.ext.upper()} ${signal_items.condition_name} ${signal_items.replicate_name} ${signal_items.experiment_type} ${frc} 163 ${signal_items.signal} Signal ${signal_items.signal.ext.upper()} ${condition_items.condition_name} ${signal_items.replicate_name} ${condition_items.experiment_type} ${frc}
164 #end for 164 #end for
165 #for $control_items in $condition_items.control_repeat: 165 #for $control_items in $condition_items.control_repeat:
166 #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes': 166 #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes':
167 #set $rn = $control_items.specify_replicate_name_cond.replicate_name 167 #set $rn = $control_items.specify_replicate_name_cond.replicate_name
168 #else: 168 #else:
171 #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes': 171 #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
172 #set $frc = $control_items.fixedreadcount_cond.fixedreadcount 172 #set $frc = $control_items.fixedreadcount_cond.fixedreadcount
173 #else: 173 #else:
174 #set $frc = '' 174 #set $frc = ''
175 #end if 175 #end if
176 ${control_items.control} Control ${control_items.control.ext.upper()} ${control_items.condition_name} ${rn} ${control_items.experiment_type} ${frc} 176 ${control_items.control} Control ${control_items.control.ext.upper()} ${condition_items.condition_name} ${rn} ${condition_items.experiment_type} ${frc}
177 #end for 177 #end for
178 #end for ]]></configfile> 178 #end for ]]></configfile>
179 </configfiles> 179 </configfiles>
180 <inputs> 180 <inputs>
181 <repeat name="condition_repeat" title="Condition" min="1"> 181 <repeat name="condition_repeat" title="Condition" min="1">
182 <param name="condition_name" type="text" value="cond" label="Condition name" />
183 <expand macro="param_experiment_type" />
182 <repeat name="signal_repeat" title="Signal" min="1"> 184 <repeat name="signal_repeat" title="Signal" min="1">
183 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx"> 185 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
184 <validator type="unspecified_build" /> 186 <validator type="unspecified_build" />
185 </param> 187 </param>
186 <expand macro="param_experiment_type" />
187 <param name="condition_name" type="text" value="cond" label="Condition name" />
188 <param name="replicate_name" type="text" value="rep" label="Replicate name" /> 188 <param name="replicate_name" type="text" value="rep" label="Replicate name" />
189 <expand macro="cond_fixedreadcount" /> 189 <expand macro="cond_fixedreadcount" />
190 </repeat> 190 </repeat>
191 <repeat name="control_repeat" title="Control" min="0"> 191 <repeat name="control_repeat" title="Control" min="0">
192 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx"> 192 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
193 <validator type="unspecified_build" /> 193 <validator type="unspecified_build" />
194 </param> 194 </param>
195 <expand macro="param_experiment_type" />
196 <param name="condition_name" type="text" value="cond" label="Condition name" />
197 <conditional name="specify_replicate_name_cond"> 195 <conditional name="specify_replicate_name_cond">
198 <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"> 196 <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">
199 <option value="no" selected="True">No</option> 197 <option value="no" selected="True">No</option>
200 <option value="yes">Yes</option> 198 <option value="yes">Yes</option>
201 </param> 199 </param>
408 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/> 406 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>
409 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/> 407 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>
410 </outputs> 408 </outputs>
411 <tests> 409 <tests>
412 <test> 410 <test>
413 <param name="single_or_multi_expt" value="single" /> 411 <repeat name="condition_repeat">
414 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 412 <repeat name="signal_repeat">
413 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
414 </repeat>
415 </repeat>
415 <param name="advanced_options" value="hide" /> 416 <param name="advanced_options" value="hide" />
416 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/> 417 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
417 <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/> 418 <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
418 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/> 419 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
419 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/> 420 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
420 </test> 421 </test>
421 <test> 422 <test>
422 <param name="single_or_multi_expt" value="single" /> 423 <repeat name="condition_repeat">
423 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 424 <repeat name="signal_repeat">
424 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" /> 425 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
426 </repeat>
427 <repeat name="control_repeat">
428 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
429 </repeat>
430 </repeat>
425 <param name="advanced_options" value="display" /> 431 <param name="advanced_options" value="display" />
426 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/> 432 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
427 <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/> 433 <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
428 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/> 434 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
429 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/> 435 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>