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comparison ideas.xml @ 112:5753c1386737 draft

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Uploaded
author greg
date Wed, 15 Nov 2017 08:57:21 -0500
parents 0c9cdefe4b45
children ba7238a53377
comparison
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111:0c9cdefe4b45 112:5753c1386737
86 #if str($maxerr) != "0.0": 86 #if str($maxerr) != "0.0":
87 -maxerr $maxerr 87 -maxerr $maxerr
88 #end if 88 #end if
89 -rseed $rseed 89 -rseed $rseed
90 -thread \${GALAXY_SLOTS:-4} 90 -thread \${GALAXY_SLOTS:-4}
91 -o '$project_name'
91 #if str($save_ideas_log) == "yes": 92 #if str($save_ideas_log) == "yes":
92 > $output_log 93 > $output_log
93 #else: 94 #else:
94 > /dev/null 95 > /dev/null
95 #end if 96 #end if
152 <validator type="unspecified_build"/> 153 <validator type="unspecified_build"/>
153 </param> 154 </param>
154 </repeat> 155 </repeat>
155 </when> 156 </when>
156 </conditional> 157 </conditional>
158 <param name="project_name" type="text" value="" optional="false" label="Project name" help="Outputs will have this base name">
159 <validator type="empty_field"/>
160 </param>
157 <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/> 161 <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/>
158 <conditional name="specify_genomic_window_cond"> 162 <conditional name="specify_genomic_window_cond">
159 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data"> 163 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
160 <option value="no" selected="true">No</option> 164 <option value="no" selected="true">No</option>
161 <option value="yes">Yes</option> 165 <option value="yes">Yes</option>
205 <outputs> 209 <outputs>
206 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}"> 210 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
207 <filter>save_ideas_log == 'yes'</filter> 211 <filter>save_ideas_log == 'yes'</filter>
208 </data> 212 </data>
209 <data name="output_heatmap" format="pdf" label="${tool.name} (heatmap) on ${on_string}"/> 213 <data name="output_heatmap" format="pdf" label="${tool.name} (heatmap) on ${on_string}"/>
210 <collection name="output" type="list"> 214 <collection name="output_txt_collection" type="list">
211 <discover_datasets pattern="__name__" directory="output_dir" format="txt"/> 215 <discover_datasets pattern="__name__" directory="output_dir" format="txt"/>
212 </collection> 216 </collection>
213 </outputs> 217 </outputs>
214 <tests> 218 <tests>
215 <test> 219 <test>
216 <param name="cell_type_epigenetic_factor" value="extract"/> 220 <param name="cell_type_epigenetic_factor" value="extract"/>
217 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/> 221 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
218 <param name="input_name_positions" value="cell_first"/> 222 <param name="input_name_positions" value="cell_first"/>
219 <param name="specify_genomic_window" value="yes"/> 223 <param name="specify_genomic_window" value="yes"/>
220 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/> 224 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
221 <output name="output_state" file="output_state.txt" ftype="txt"/> 225 <output_collection name="output_txt_collection" type="list">
222 <output name="output_profile" file="output_profile.txt" ftype="txt"/> 226 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
223 <output name="output_para" file="output_para.txt" ftype="txt"/> 227 <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/>
224 <output name="output_cluster" file="output_cluster.txt" ftype="txt"/> 228 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
225 <output_collection name="primary_fna" type="list"> 229 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
226 <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
227 <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
228 <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
229 </output_collection> 230 </output_collection>
231 <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/>
230 </test> 232 </test>
231 <test> 233 <test>
232 <param name="cell_type_epigenetic_factor" value="manual"/> 234 <param name="cell_type_epigenetic_factor" value="manual"/>
233 <repeat name="input_repeat"> 235 <repeat name="input_repeat">
234 <param name="cell_type_name" value="e001" /> 236 <param name="cell_type_name" value="e001" />
235 <param name="epigenetic_factor_name" value="h3k4me3"/> 237 <param name="epigenetic_factor_name" value="h3k4me3"/>
236 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/> 238 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
237 </repeat> 239 </repeat>
238 <param name="specify_genomic_window" value="yes"/> 240 <param name="specify_genomic_window" value="yes"/>
239 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/> 241 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
240 <output name="output_state" file="output_state.txt" ftype="txt"/> 242 <output_collection name="output_txt_collection" type="list">
241 <output name="output_profile" file="output_profile.txt" ftype="txt"/> 243 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
242 <output name="output_para" file="output_para.txt" ftype="txt"/> 244 <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/>
243 <output name="output_cluster" file="output_cluster.txt" ftype="txt"/> 245 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
246 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
247 </output_collection>
248 <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/>
244 </test> 249 </test>
245 </tests> 250 </tests>
246 <help> 251 <help>
247 **What it does** 252 **What it does**
248 253