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comparison ideas.xml @ 34:8d8f796a3bda draft

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Uploaded
author greg
date Tue, 22 Aug 2017 11:06:22 -0400
parents 695053a23fe4
children b287aae59e1d
comparison
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33:695053a23fe4 34:8d8f796a3bda
44 #set outputs_by_chr = $outputs_by_chr_cond.outputs_by_chr 44 #set outputs_by_chr = $outputs_by_chr_cond.outputs_by_chr
45 #if str($outputs_by_chr) == 'yes': 45 #if str($outputs_by_chr) == 'yes':
46 -bychr 46 -bychr
47 #end if 47 #end if
48 -c $reads_per_bp 48 -c $reads_per_bp
49 #set blacklist_regions = $blacklist_regions_cond.blacklist_regions 49 #if str($blacklist_input) not in ['None', '']:
50 #if str($blacklist_regions) == 'yes': 50 -exclude '$blacklist_input'
51 -exclude '$blacklist_regions_cond.blacklist_input'
52 #end if 51 #end if
53 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets 52 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets
54 #if str($standardize_datasets) == 'yes': 53 #if str($standardize_datasets) == 'yes':
55 -norm 54 -norm
56 #end if 55 #end if
195 <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" help="Zero value has no affect"/> 194 <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" help="Zero value has no affect"/>
196 <param name="initial_states" type="integer" value="20" min="1" label="Initial number of states" help="Zero value has no affect"/> 195 <param name="initial_states" type="integer" value="20" min="1" label="Initial number of states" help="Zero value has no affect"/>
197 <param name="max_position_classes" type="integer" value="0" min="0" label="Maximum number of position classes to be inferred" help="Zero value has no affect"/> 196 <param name="max_position_classes" type="integer" value="0" min="0" label="Maximum number of position classes to be inferred" help="Zero value has no affect"/>
198 <param name="max_cell_type_clusters" type="integer" value="0" min="0" label="Maximum number of cell type clusters allowed" help="Zero value has no affect"/> 197 <param name="max_cell_type_clusters" type="integer" value="0" min="0" label="Maximum number of cell type clusters allowed" help="Zero value has no affect"/>
199 <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default value: sqrt(number of cell types)"/> 198 <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default value: sqrt(number of cell types)"/>
200 <param name="burnin_num" type="integer" value="50" min="1" label="Number of burnin steps"/> 199 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/>
201 <param name="mcmc_num" type="integer" value="50" min="1" label="Number of maximization steps"/> 200 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/>
202 <param name="min_standard_dev" type="float" value="0.5" min="0" label="Minimum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 0.5"/> 201 <param name="min_standard_dev" type="float" value="0.5" min="0" label="Minimum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 0.5"/>
203 <param name="max_standard_dev" type="float" value="1000000" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: infinity"/> 202 <param name="max_standard_dev" type="float" value="0" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: infinity"/>
204 </inputs> 203 </inputs>
205 <outputs> 204 <outputs>
206 <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}"/> 205 <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}"/>
207 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/> 206 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/>
208 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/> 207 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/>