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comparison multigps.xml @ 41:d08ca1690fa1 draft

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Uploaded
author iuc
date Thu, 06 Apr 2017 10:54:38 -0400
parents 9d4d90d4458a
children b8995d2a0341
comparison
equal deleted inserted replaced
40:9d4d90d4458a 41:d08ca1690fa1
144 --diffp $rbec.diffp 144 --diffp $rbec.diffp
145 #end if 145 #end if
146 #end if 146 #end if
147 2>&1 147 2>&1
148 --out '$output_html.files_path' 148 --out '$output_html.files_path'
149 #if str($output_design_file) == 'yes':
150 && mv '$build_design_file' '$output_design_file'
151 #end if
149 && mv $output_dir/*.counts '$replicates_counts' 152 && mv $output_dir/*.counts '$replicates_counts'
150 && mv $output_dir/*.bed '$output_bed' 153 && mv $output_dir/*.bed '$output_bed'
151 && mv $output_dir/*.html '$output_html' 154 && mv $output_dir/*.html '$output_html'
152 && mv $output_dir/*.table.txt '$all_events_table' 155 && mv $output_dir/*.table.txt '$all_events_table'
153 ]]> 156 ]]>
177 #end for 180 #end for
178 #end for ]]></configfile> 181 #end for ]]></configfile>
179 </configfiles> 182 </configfiles>
180 <inputs> 183 <inputs>
181 <repeat name="condition_repeat" title="Condition" min="1"> 184 <repeat name="condition_repeat" title="Condition" min="1">
182 <param name="condition_name" type="text" value="cond" label="Condition name" /> 185 <param name="condition_name" type="text" value="cond" label="Condition name">
186 <validator type="empty_field" />
187 </param>
183 <expand macro="param_experiment_type" /> 188 <expand macro="param_experiment_type" />
184 <repeat name="signal_repeat" title="Signal" min="1"> 189 <repeat name="signal_repeat" title="Signal" min="1">
185 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx"> 190 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
186 <validator type="unspecified_build" /> 191 <validator type="unspecified_build" />
187 </param> 192 </param>
188 <param name="replicate_name" type="text" value="rep" label="Replicate name" /> 193 <param name="replicate_name" type="text" value="1" label="Replicate name">
194 <validator type="empty_field" />
195 </param>
189 <expand macro="cond_fixedreadcount" /> 196 <expand macro="cond_fixedreadcount" />
190 </repeat> 197 </repeat>
191 <repeat name="control_repeat" title="Control" min="0"> 198 <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"> 199 <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" /> 200 <validator type="unspecified_build" />
203 <when value="no" /> 210 <when value="no" />
204 </conditional> 211 </conditional>
205 <expand macro="cond_fixedreadcount" /> 212 <expand macro="cond_fixedreadcount" />
206 </repeat> 213 </repeat>
207 </repeat> 214 </repeat>
215 <param name="output_design_file" type="select" display="radio" label="Output design file?">
216 <option value="no" selected="true">No</option>
217 <option value="yes">Yes</option>
218 </param>
208 <!-- Advanced options --> 219 <!-- Advanced options -->
209 <conditional name="advanced_options_cond"> 220 <conditional name="advanced_options_cond">
210 <param name="advanced_options" type="select" label="Advanced options"> 221 <param name="advanced_options" type="select" label="Advanced options">
211 <option value="hide" selected="true">Hide</option> 222 <option value="hide" selected="true">Hide</option>
212 <option value="display">Display</option> 223 <option value="display">Display</option>
399 </when> 410 </when>
400 <when value="hide" /> 411 <when value="hide" />
401 </conditional> 412 </conditional>
402 </inputs> 413 </inputs>
403 <outputs> 414 <outputs>
415 <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
416 <filter>output_design_file == 'yes'</filter>
417 </data>
404 <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/> 418 <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>
405 <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/> 419 <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>
406 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/> 420 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>
407 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/> 421 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>
408 </outputs> 422 </outputs>