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comparison ideas.xml @ 45:25f82826cfa1 draft

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Uploaded
author greg
date Wed, 23 Aug 2017 09:12:33 -0400
parents 8e449b51b581
children f93c1cfb9e0a
comparison
equal deleted inserted replaced
44:8e449b51b581 45:25f82826cfa1
39 #end for 39 #end for
40 -chr ",".join(chroms) 40 -chr ",".join(chroms)
41 #end if 41 #end if
42 #end if 42 #end if
43 #end if 43 #end if
44 #set outputs_by_chr = $outputs_by_chr_cond.outputs_by_chr 44 $bychr
45 #if str($outputs_by_chr) == 'yes':
46 -bychr
47 #end if
48 -c $reads_per_bp 45 -c $reads_per_bp
49 #if str($blacklist_input) not in ['None', '']: 46 #if str($blacklist_input) not in ['None', '']:
50 -exclude '$blacklist_input' 47 -exclude '$blacklist_input'
51 #end if 48 #end if
52 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets 49 $norm
53 #if str($standardize_datasets) == 'yes':
54 -norm
55 #end if
56 ############################################## 50 ##############################################
57 ## Coerce the prepMat config output to the 51 ## Coerce the prepMat config output to the
58 ## format expected by the R matrix builder. 52 ## format expected by the R matrix builder.
59 ############################################## 53 ##############################################
60 && cut -d' ' $prep_input_config -f1,2 > file1.txt 54 && cut -d' ' $prep_input_config -f1,2 > file1.txt
70 ############################################## 64 ##############################################
71 ## Run IDEAS 65 ## Run IDEAS
72 ############################################## 66 ##############################################
73 && ideas 67 && ideas
74 '$prep_output_config' 68 '$prep_output_config'
75 $tmp_dir/*.bed 69 #if str($input_type) == 'datasets':
70 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
71 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
72 if str($specify_genomic_window) == 'yes':
73 '$specify_genomic_window_cond.bed_input'
74 #else:
75 $tmp_dir/*.bed
76 #end if
77 #else:
78 $tmp_dir/*.bed
79 #end if
76 $hp 80 $hp
77 #if str($log2_num) != '0.0': 81 $log2
78 -log2 $log2_num
79 #end if
80 #if str($max_states) != '0.0': 82 #if str($max_states) != '0.0':
81 -G $max_states 83 -G $max_states
82 #end if 84 #end if
83 #if str($initial_states) != '0.0': 85 #if str($initial_states) != '0':
84 -C $initial_states 86 -C $initial_states
85 #end if 87 #end if
86 #if str($max_position_classes) != '0': 88 #if str($max_position_classes) != '0':
87 -P $max_position_classes 89 -P $max_position_classes
88 #end if 90 #end if
91 #end if 93 #end if
92 #if str($prior_concentration) != '0.0': 94 #if str($prior_concentration) != '0.0':
93 -A $prior_concentration 95 -A $prior_concentration
94 #end if 96 #end if
95 -sample $burnin_num $mcmc_num 97 -sample $burnin_num $mcmc_num
96 #if str($min_standard_dev) != '0.0': 98 #if str($minerr) != '0.0':
97 -minerr $min_standard_dev 99 -minerr $minerr
98 #end if 100 #end if
99 #if str($max_standard_dev) != '0.0': 101 #if str($maxerr) != '0.0':
100 -maxerr $max_standard_dev 102 -maxerr $maxerr
101 #end if 103 #end if
102 -thread \${GALAXY_SLOTS:-4} 104 -thread \${GALAXY_SLOTS:-4}
103 > $output_log 105 > $output_log
104 && mv ./*.cluster $output_cluster 106 && mv ./*.cluster $output_cluster
105 && mv ./*.para $output_para 107 && mv ./*.para $output_para
155 </when> 157 </when>
156 </conditional> 158 </conditional>
157 </when> 159 </when>
158 <when value="data_matrix"/> 160 <when value="data_matrix"/>
159 </conditional> 161 </conditional>
160 <conditional name="outputs_by_chr_cond"> 162 <param argument="-bychr" type="boolean" truevalue="-bychr" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
161 <param name="outputs_by_chr" type="select" display="radio" label="Output chromosomes in separate files">
162 <option value="no" selected="true">No</option>
163 <option value="yes">Yes</option>
164 </param>
165 <when value="no"/>
166 <when value="yes"/>
167 </conditional>
168 <param name="reads_per_bp" type="select" display="radio" label="Calculate the average signal in each genomic window using"> 163 <param name="reads_per_bp" type="select" display="radio" label="Calculate the average signal in each genomic window using">
169 <option value="6" selected="true">mean</option> 164 <option value="6" selected="true">mean</option>
170 <option value="8">max</option> 165 <option value="8">max</option>
171 </param> 166 </param>
172 <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/> 167 <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
173 <conditional name="standardize_datasets_cond"> 168 <param argument="-norm" type="boolean" truevalue="-norm" falsevalue="" checked="False" label="Standardize all datasets"/>
174 <param name="standardize_datasets" type="select" display="radio" label="Standardize all datasets">
175 <option value="no" selected="true">No</option>
176 <option value="yes">Yes</option>
177 </param>
178 <when value="no"/>
179 <when value="yes"/>
180 </conditional>
181 <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/> 169 <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/>
182 <param name="log2_num" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/> 170 <param argument="-log2" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/>
183 <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" 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"/>
184 <param name="initial_states" type="integer" value="20" min="1" label="Initial number of states" 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"/>
185 <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"/> 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"/>
186 <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"/> 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"/>
187 <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)"/> 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)"/>
188 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/> 176 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/>
189 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/> 177 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/>
190 <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"/> 178 <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"/>
191 <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: 1000000"/> 179 <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"/>
192 </inputs> 180 </inputs>
193 <outputs> 181 <outputs>
194 <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}"/> 182 <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}"/>
195 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/> 183 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/>
196 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/> 184 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/>