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comparison ideas.xml @ 89:d6ab97fb8aca draft

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author greg
date Fri, 25 Aug 2017 12:22:59 -0400
parents 462ce06410c6
children 029e18c3c17b
comparison
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88:462ce06410c6 89:d6ab97fb8aca
101 #end if 101 #end if
102 #if str($maxerr) != "0.0": 102 #if str($maxerr) != "0.0":
103 -maxerr $maxerr 103 -maxerr $maxerr
104 #end if 104 #end if
105 -thread \${GALAXY_SLOTS:-4} 105 -thread \${GALAXY_SLOTS:-4}
106 > $output_log 106 #if str($save_ideas_log) == "yes":
107 > $output_log
108 #else:
109 > /dev/null
110 #end if
107 && mv ./*.cluster $output_cluster 111 && mv ./*.cluster $output_cluster
108 && mv ./*.para $output_para 112 && mv ./*.para $output_para
109 && mv ./*.profile $output_profile 113 && mv ./*.profile $output_profile
110 && mv ./*.state $output_state 114 && mv ./*.state $output_state
111 ]]></command> 115 ]]></command>
215 <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default value: sqrt(number of cell types)"/> 219 <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default value: sqrt(number of cell types)"/>
216 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/> 220 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/>
217 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/> 221 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/>
218 <param name="minerr" type="float" value="0.5" min="0" label="Minimum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 0.5"/> 222 <param name="minerr" type="float" value="0.5" min="0" label="Minimum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 0.5"/>
219 <param name="maxerr" type="float" value="1000000" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 1000000"/> 223 <param name="maxerr" type="float" value="1000000" min="0" label="Maximum standard deviation for the emission Gaussian distribution" help="Zero value results in the default value: 1000000"/>
224 <param name="save_ideas_log" type="select" display="radio" label="Save IDEAS log in an additional history item">
225 <option value="no" selected="true">No</option>
226 <option value="yes">Yes</option>
227 </param>
220 </inputs> 228 </inputs>
221 <outputs> 229 <outputs>
222 <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}"/> 230 <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}">
231 <filter>save_ideas_log == 'yes'</filter>
232 </data>
223 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/> 233 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/>
224 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/> 234 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/>
225 <data name="output_profile" format="txt" label="${tool.name} (profile) on ${on_string}"/> 235 <data name="output_profile" format="txt" label="${tool.name} (profile) on ${on_string}"/>
226 <data name="output_state" format="txt" label="${tool.name} (epigenetic states and position classes) on ${on_string}"/> 236 <data name="output_state" format="txt" label="${tool.name} (epigenetic states and position classes) on ${on_string}"/>
227 </outputs> 237 </outputs>