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comparison ideas.xml @ 44:8e449b51b581 draft

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author greg
date Wed, 23 Aug 2017 08:45:14 -0400
parents 9264225d796d
children 25f82826cfa1
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43:9264225d796d 44:8e449b51b581
24 #if str($input_type) == 'datasets': 24 #if str($input_type) == 'datasets':
25 '$prep_input_config' 25 '$prep_input_config'
26 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 26 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
27 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 27 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
28 #if str($specify_genomic_window) == 'yes': 28 #if str($specify_genomic_window) == 'yes':
29 -bed '$bed_input' 29 -bed '$specify_genomic_window_cond.bed_input'
30 #else: 30 #else:
31 -gsz '$chromInfo' 31 -gsz '$chromInfo'
32 -wsz $specify_genomic_window_cond.window_size 32 -wsz $specify_genomic_window_cond.window_size
33 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes 33 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
34 #if str($restrict_chromosomes) == 'yes': 34 #if str($restrict_chromosomes) == 'yes':
71 ## Run IDEAS 71 ## Run IDEAS
72 ############################################## 72 ##############################################
73 && ideas 73 && ideas
74 '$prep_output_config' 74 '$prep_output_config'
75 $tmp_dir/*.bed 75 $tmp_dir/*.bed
76 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation 76 $hp
77 #if str($smoother_annotation) == 'yes':
78 -hp
79 #end if
80 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
81 #if str($smoother_annotation) == 'yes':
82 -hp
83 #end if
84 #if str($log2_num) != '0.0': 77 #if str($log2_num) != '0.0':
85 -log2 $log2_num 78 -log2 $log2_num
86 #end if 79 #end if
87 #if str($max_states) != '0.0': 80 #if str($max_states) != '0.0':
88 -G $max_states 81 -G $max_states
163 </conditional> 156 </conditional>
164 </when> 157 </when>
165 <when value="data_matrix"/> 158 <when value="data_matrix"/>
166 </conditional> 159 </conditional>
167 <conditional name="outputs_by_chr_cond"> 160 <conditional name="outputs_by_chr_cond">
168 <param name="outputs_by_chr" type="select" display="radio" label="Output chromosomes in seperate files"> 161 <param name="outputs_by_chr" type="select" display="radio" label="Output chromosomes in separate files">
169 <option value="no" selected="true">No</option> 162 <option value="no" selected="true">No</option>
170 <option value="yes">Yes</option> 163 <option value="yes">Yes</option>
171 </param> 164 </param>
172 <when value="no"/> 165 <when value="no"/>
173 <when value="yes"/> 166 <when value="yes"/>
183 <option value="yes">Yes</option> 176 <option value="yes">Yes</option>
184 </param> 177 </param>
185 <when value="no"/> 178 <when value="no"/>
186 <when value="yes"/> 179 <when value="yes"/>
187 </conditional> 180 </conditional>
188 <conditional name="smoother_annotation_cond"> 181 <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/>
189 <param name="smoother_annotation" type="select" display="radio" label="Discourage state transition across chromosomes">
190 <option value="no" selected="true">No</option>
191 <option value="yes">Yes</option>
192 </param>
193 <when value="no"/>
194 <when value="yes"/>
195 </conditional>
196 <param name="log2_num" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/> 182 <param name="log2_num" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/>
197 <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" 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"/>
198 <param name="initial_states" type="integer" value="20" min="1" label="Initial number of states" 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"/>
199 <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"/> 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"/>
200 <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"/> 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"/>
244 230
245 * **Bed file specifying the genomic windows** - bed file specifying the genomic windows (if "Yes" is selected) 231 * **Bed file specifying the genomic windows** - bed file specifying the genomic windows (if "Yes" is selected)
246 232
247 **Other options** 233 **Other options**
248 234
249 * **Output chromosomes in seperate files** - select "Yes" to produce seperate files for each chromosome, allowing you to run IDEAS on different chromosomes separately. 235 * **Output chromosomes in separate files** - select "Yes" to produce separate files for each chromosome, allowing you to run IDEAS on different chromosomes separately.
250 * **Calculate the average signal in each genomic window using** - use the bigWigAverageOverBed utility from the UCSC genome browser to calculate average signal (number of reads per bp) in each genomic window. 236 * **Calculate the average signal in each genomic window using** - use the bigWigAverageOverBed utility from the UCSC genome browser to calculate average signal (number of reads per bp) in each genomic window.
251 * **Select file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets. 237 * **Select file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets.
252 * **Standardize all datasets** - select "Yes" to standardize all datasets (e.g., reads / total_reads * 20 million) so that the signals from different cell types become comparable - your datasets can be read counts, logp-values or fold change. 238 * **Standardize all datasets** - select "Yes" to standardize all datasets (e.g., reads / total_reads * 20 million) so that the signals from different cell types become comparable - your datasets can be read counts, logp-values or fold change.
253 239
254 * **Discourage state transition across chromosomes** - select "Yes" to produce similar states in adjacent windows, making the annotation smoother, but at risk of reducing precision. 240 * **Discourage state transition across chromosomes** - select "Yes" to produce similar states in adjacent windows, making the annotation smoother, but at risk of reducing precision.