Mercurial > repos > greg > ideas
diff ideas.xml @ 101:ad45c3ba16b2 draft
Uploaded
author | greg |
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date | Wed, 08 Nov 2017 07:45:52 -0500 |
parents | 86445eab5f51 |
children | dad89ec8846f |
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--- a/ideas.xml Mon Oct 16 08:24:05 2017 -0400 +++ b/ideas.xml Wed Nov 08 07:45:52 2017 -0500 @@ -183,16 +183,16 @@ <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/> <param argument="-norm" type="boolean" truevalue="-norm" falsevalue="" checked="False" label="Standardize all datasets"/> <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/> - <param name="log2" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/> - <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" help="Zero value has no affect"/> - <param name="initial_states" type="integer" value="20" min="0" label="Initial number of states" help="Zero value has no affect"/> - <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"/> - <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"/> - <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)"/> + <param name="log2" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero means no log2 transformation"/> + <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" help="Zero sets the maximum to a large number"/> + <param name="initial_states" type="integer" value="20" min="0" label="Initial number of states" help="Positive integer"/> + <param name="max_position_classes" type="integer" value="0" min="0" label="Maximum number of position classes to be inferred" help="Zero sets the maximum to a large number"/> + <param name="max_cell_type_clusters" type="integer" value="0" min="0" label="Maximum number of cell type clusters allowed" help="Zero sets the maximum to a large number"/> + <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default: sqrt(number of cell types)"/> <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/> <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/> - <param name="minerr" 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"/> - <param name="maxerr" type="float" value="1000000" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 1000000"/> + <param name="minerr" type="float" value="0.5" min="0" label="Minimum standard deviation for the emission Gaussian distribution" help="Zero value results in the default: 0.5"/> + <param name="maxerr" type="float" value="1000000" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero sets the maximum to a large number"/> <param name="save_ideas_log" type="select" display="radio" label="Save IDEAS log in an additional history item"> <option value="no" selected="true">No</option> <option value="yes">Yes</option>