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comparison ideas.xml @ 102:dad89ec8846f draft

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Uploaded
author greg
date Tue, 14 Nov 2017 08:22:33 -0500
parents ad45c3ba16b2
children 705c4f8fbefd
comparison
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101:ad45c3ba16b2 102:dad89ec8846f
89 #if str($save_ideas_log) == "yes": 89 #if str($save_ideas_log) == "yes":
90 > $output_log 90 > $output_log
91 #else: 91 #else:
92 > /dev/null 92 > /dev/null
93 #end if 93 #end if
94 && mv ./*.cluster $output_cluster
95 && mv ./*.para $output_para
96 && mv ./*.profile $output_profile
97 && mv ./*.state $output_state
98 ]]></command> 94 ]]></command>
99 <configfiles> 95 <configfiles>
100 <configfile name="gen_prep_input_config"><![CDATA[#import os 96 <configfile name="gen_prep_input_config"><![CDATA[#import os
101 #if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 97 #if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
102 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 98 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
197 <option value="no" selected="true">No</option> 193 <option value="no" selected="true">No</option>
198 <option value="yes">Yes</option> 194 <option value="yes">Yes</option>
199 </param> 195 </param>
200 </inputs> 196 </inputs>
201 <outputs> 197 <outputs>
202 <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}"> 198 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
203 <filter>save_ideas_log == 'yes'</filter> 199 <filter>save_ideas_log == 'yes'</filter>
204 </data> 200 </data>
205 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/> 201 <collection name="output" type="list">
206 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/> 202 <discover_datasets pattern="__name__" format="txt"/>
207 <data name="output_profile" format="txt" label="${tool.name} (profile) on ${on_string}"/> 203 </collection>
208 <data name="output_state" format="txt" label="${tool.name} (epigenetic states and position classes) on ${on_string}"/>
209 </outputs> 204 </outputs>
210 <tests> 205 <tests>
211 <test> 206 <test>
212 <param name="cell_type_epigenetic_factor" value="extract"/> 207 <param name="cell_type_epigenetic_factor" value="extract"/>
213 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/> 208 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
214 <param name="input_name_positions" value="cell_first"/> 209 <param name="input_name_positions" value="cell_first"/>
215 <param name="specify_genomic_window" value="yes"/> 210 <param name="specify_genomic_window" value="yes"/>
216 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/> 211 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
217 <output name="output_state" file="output_state.txt" ftype="txt"/> 212 <output name="output_state" file="output_state.txt" ftype="txt"/>
218 <output name="output_profile" file="output_profile.txt" ftype="txt"/> 213 <output name="output_profile" file="output_profile.txt" ftype="txt"/>
219 <output name="output_para" file="output_para.tabular" ftype="tabular"/> 214 <output name="output_para" file="output_para.txt" ftype="txt"/>
220 <output name="output_cluster" file="output_cluster.txt" ftype="txt"/> 215 <output name="output_cluster" file="output_cluster.txt" ftype="txt"/>
216 <output_collection name="primary_fna" type="list">
217 <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
218 <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
219 <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
220 </output_collection>
221
221 </test> 222 </test>
222 <test> 223 <test>
223 <param name="cell_type_epigenetic_factor" value="manual"/> 224 <param name="cell_type_epigenetic_factor" value="manual"/>
224 <repeat name="input_repeat"> 225 <repeat name="input_repeat">
225 <param name="cell_type_name" value="e001" /> 226 <param name="cell_type_name" value="e001" />
228 </repeat> 229 </repeat>
229 <param name="specify_genomic_window" value="yes"/> 230 <param name="specify_genomic_window" value="yes"/>
230 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/> 231 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
231 <output name="output_state" file="output_state.txt" ftype="txt"/> 232 <output name="output_state" file="output_state.txt" ftype="txt"/>
232 <output name="output_profile" file="output_profile.txt" ftype="txt"/> 233 <output name="output_profile" file="output_profile.txt" ftype="txt"/>
233 <output name="output_para" file="output_para.tabular" ftype="tabular"/> 234 <output name="output_para" file="output_para.txt" ftype="txt"/>
234 <output name="output_cluster" file="output_cluster.txt" ftype="txt"/> 235 <output name="output_cluster" file="output_cluster.txt" ftype="txt"/>
235 </test> 236 </test>
236 </tests> 237 </tests>
237 <help> 238 <help>
238 **What it does** 239 **What it does**