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comparison ideas.xml @ 47:3a4697f71a05 draft

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Uploaded
author greg
date Wed, 23 Aug 2017 09:20:45 -0400
parents f93c1cfb9e0a
children c9c90bfbeb20
comparison
equal deleted inserted replaced
46:f93c1cfb9e0a 47:3a4697f71a05
76 #end if 76 #end if
77 #else: 77 #else:
78 $tmp_dir/*.bed 78 $tmp_dir/*.bed
79 #end if 79 #end if
80 $hp 80 $hp
81 $log2 81 #if str($log2) != '0.0':
82 -log2 $log2
83 #end if
82 #if str($max_states) != '0.0': 84 #if str($max_states) != '0.0':
83 -G $max_states 85 -G $max_states
84 #end if 86 #end if
85 #if str($initial_states) != '0': 87 #if str($initial_states) != '0':
86 -C $initial_states 88 -C $initial_states
165 <option value="8">max</option> 167 <option value="8">max</option>
166 </param> 168 </param>
167 <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/> 169 <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
168 <param argument="-norm" type="boolean" truevalue="-norm" falsevalue="" checked="False" label="Standardize all datasets"/> 170 <param argument="-norm" type="boolean" truevalue="-norm" falsevalue="" checked="False" label="Standardize all datasets"/>
169 <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/> 171 <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/>
170 <param argument="-log2" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/> 172 <param name="log2" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/>
171 <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" help="Zero value has no affect"/> 173 <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" help="Zero value has no affect"/>
172 <param name="initial_states" type="integer" value="20" min="0" label="Initial number of states" help="Zero value has no affect"/> 174 <param name="initial_states" type="integer" value="20" min="0" label="Initial number of states" help="Zero value has no affect"/>
173 <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"/> 175 <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"/>
174 <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"/> 176 <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"/>
175 <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)"/> 177 <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)"/>