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comparison ideas.xml @ 149:a80b76535243 draft

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Uploaded
author greg
date Fri, 12 Jan 2018 11:24:30 -0500
parents 8cfcf32c4282
children 9d34f7e6d80c
comparison
equal deleted inserted replaced
148:0ba72d5ca209 149:a80b76535243
12 #set output_pdf_dir = "output_pdf_dir" 12 #set output_pdf_dir = "output_pdf_dir"
13 #set output_txt_dir = "output_txt_dir" 13 #set output_txt_dir = "output_txt_dir"
14 #set tmp_dir = "tmp" 14 #set tmp_dir = "tmp"
15 #set prep_input_config = "prep_input_config.txt" 15 #set prep_input_config = "prep_input_config.txt"
16 #set prep_output_config = "prep_output_config.txt" 16 #set prep_output_config = "prep_output_config.txt"
17 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
18 #set perform_training = $perform_training_cond.perform_training
17 ############################################## 19 ##############################################
18 ## Create the config file and prepare the data 20 ## Create the config file and prepare the data
19 ############################################## 21 ##############################################
20 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
21 #if str($output_heatmaps) == "yes": 22 #if str($output_heatmaps) == "yes":
22 mkdir '$output_pdf_dir' && 23 mkdir '$output_pdf_dir' &&
23 #end if 24 #end if
24 mkdir '$output_txt_dir' && 25 mkdir '$output_txt_dir' &&
25 cp '$gen_prep_input_config' $prep_input_config && 26 cp '$gen_prep_input_config' $prep_input_config &&
80 #else: 81 #else:
81 #set $window_positions_by_chroms[$items[0]] = [$count, $count+1] 82 #set $window_positions_by_chroms[$items[0]] = [$count, $count+1]
82 #end if 83 #end if
83 #end for 84 #end for
84 #for chrom, tup in $window_positions_by_chroms.items(): 85 #for chrom, tup in $window_positions_by_chroms.items():
85 && ideas 86 && Rscript '$__tool_directory__/ideas.R'
86 '$prep_output_config' 87 #if str($perform_training) == "yes":
87 '$specify_genomic_window_cond.bed_input' 88 --training_iterations $perform_training_cond.training_iterations
88 $hp 89 --training_windows $perform_training_cond.training_windows
89 -inv $tup[0] $tup[1] 90 #end if
91 --prep_output_config '$prep_output_config'
92 --windows_bed '$specify_genomic_window_cond.bed_input'
93 --hp $hp
94 --window_start $tup[0]
95 --window_end $tup[1]
90 #if str($log2) != "0.0": 96 #if str($log2) != "0.0":
91 -log2 $log2 97 --log2 $log2
92 #end if 98 #end if
93 #if str($max_states) != "0.0": 99 #if str($max_states) != "0.0":
94 -G $max_states 100 --max_states $max_states
95 #end if 101 #end if
96 #if str($initial_states) != "0": 102 #if str($initial_states) != "0":
97 -C $initial_states 103 --initial_states $initial_states
98 #end if 104 #end if
99 #if str($max_position_classes) != "0": 105 #if str($max_position_classes) != "0":
100 -P $max_position_classes 106 --max_position_classes $max_position_classes
101 #end if 107 #end if
102 #if str($max_cell_type_clusters) != "0": 108 #if str($max_cell_type_clusters) != "0":
103 -K $max_cell_type_clusters 109 --max_cell_type_clusters $max_cell_type_clusters
104 #end if 110 #end if
105 #if str($prior_concentration) != "0.0": 111 #if str($prior_concentration) != "0.0":
106 -A $prior_concentration 112 --prior_concentration $prior_concentration
107 #end if 113 #end if
108 -sample $burnin_num $mcmc_num 114 --burnin_num $burnin_num
115 --mcmc_num $mcmc_num
109 #if str($minerr) != "0.0": 116 #if str($minerr) != "0.0":
110 -minerr $minerr 117 --minerr $minerr
111 #end if 118 #end if
112 #if str($maxerr) != "0.0": 119 #if str($maxerr) != "0.0":
113 -maxerr $maxerr 120 --maxerr $maxerr
114 #end if 121 #end if
115 -rseed $rseed 122 --rseed $rseed
116 -thread \${GALAXY_SLOTS:-4} 123 --thread \${GALAXY_SLOTS:-4}
117 -o '$project_name.$chrom' 124 --project_name '$project_name.$chrom'
125 --save_ideas_log $save_ideas_log
118 #if str($save_ideas_log) == "yes": 126 #if str($save_ideas_log) == "yes":
119 &>>'$output_log'; 127 --output_log '$output_log'
120 if [[ $? -ne 0 ]]; then
121 exit 1;
122 fi
123 #else:
124 &>>ideas_log.txt;
125 if [[ $? -ne 0 ]]; then
126 cp ideas_log.txt '$output_txt_dir'
127 exit 1;
128 fi
129 #end if 128 #end if
130 #end for 129 #end for
131 #else: 130 #else:
132 ############################################## 131 ##############################################
133 ## Not using a genomic window bed file. 132 ## Not using a genomic window bed file.
134 ############################################## 133 ##############################################
135 && ideas 134 && Rscript '$__tool_directory__/ideas.R'
136 '$prep_output_config' 135 #if str($perform_training) == "yes":
137 $tmp_dir/*.bed 136 --training_iterations $perform_training_cond.training_iterations
138 $hp 137 --training_windows $perform_training_cond.training_windows
138 #end if
139 --prep_output_config '$prep_output_config'
140 --windows_bed $tmp_dir/*.bed
141 --hp $hp
139 #if str($log2) != "0.0": 142 #if str($log2) != "0.0":
140 -log2 $log2 143 --log2 $log2
141 #end if 144 #end if
142 #if str($max_states) != "0.0": 145 #if str($max_states) != "0.0":
143 -G $max_states 146 --max_states $max_states
144 #end if 147 #end if
145 #if str($initial_states) != "0": 148 #if str($initial_states) != "0":
146 -C $initial_states 149 --initial_states $initial_states
147 #end if 150 #end if
148 #if str($max_position_classes) != "0": 151 #if str($max_position_classes) != "0":
149 -P $max_position_classes 152 --max_position_classes $max_position_classes
150 #end if 153 #end if
151 #if str($max_cell_type_clusters) != "0": 154 #if str($max_cell_type_clusters) != "0":
152 -K $max_cell_type_clusters 155 --max_cell_type_clusters $max_cell_type_clusters
153 #end if 156 #end if
154 #if str($prior_concentration) != "0.0": 157 #if str($prior_concentration) != "0.0":
155 -A $prior_concentration 158 --prior_concentration $prior_concentration
156 #end if 159 #end if
157 -sample $burnin_num $mcmc_num 160 --burnin_num $burnin_num
161 --mcmc_num $mcmc_num
158 #if str($minerr) != "0.0": 162 #if str($minerr) != "0.0":
159 -minerr $minerr 163 --minerr $minerr
160 #end if 164 #end if
161 #if str($maxerr) != "0.0": 165 #if str($maxerr) != "0.0":
162 -maxerr $maxerr 166 --maxerr $maxerr
163 #end if 167 #end if
164 -rseed $rseed 168 --rseed $rseed
165 -thread \${GALAXY_SLOTS:-4} 169 --thread \${GALAXY_SLOTS:-4}
166 -o '$project_name' 170 --project_name '$project_name'
171 --save_ideas_log $save_ideas_log
167 #if str($save_ideas_log) == "yes": 172 #if str($save_ideas_log) == "yes":
168 &>'$output_log'; 173 --output_log '$output_log'
169 if [[ $? -ne 0 ]]; then
170 exit 1;
171 fi
172 #else:
173 &>ideas_log.txt;
174 if [[ $? -ne 0 ]]; then
175 cp ideas_log.txt '$output_txt_dir'
176 exit 1;
177 fi
178 #end if 174 #end if
179 #end if 175 #end if
180 && mv ./*.cluster '$output_txt_dir' 176 && mv ./*.cluster '$output_txt_dir'
181 && mv ./*.para '$output_txt_dir' 177 && mv ./*.para '$output_txt_dir'
182 && mv ./*.profile '$output_txt_dir' 178 && mv ./*.profile '$output_txt_dir'
212 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 208 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
213 #end for 209 #end for
214 #end if]]></configfile> 210 #end if]]></configfile>
215 </configfiles> 211 </configfiles>
216 <inputs> 212 <inputs>
213 <conditional name="perform_training_cond">
214 <param name="perform_training" type="select" label="Perform training?">
215 <option value="yes" selected="true">Yes</option>
216 <option value="no">No</option>
217 </param>
218 <when value="yes">
219 <param name="training_iterations" type="integer" value="20" min="1" label="Number of training iterations"/>
220 <param name="training_windows" type="integer" value="10000" min="1" label="Number of randomly selected windows for training"/>
221 </when>
222 <when value="no"/>
223 </conditional>
217 <conditional name="cell_type_epigenetic_factor_cond"> 224 <conditional name="cell_type_epigenetic_factor_cond">
218 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by"> 225 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
219 <option value="extract" selected="true">extracting them from the selected input file names</option> 226 <option value="extract" selected="true">extracting them from the selected input file names</option>
220 <option value="manual">manually setting them for each selected input</option> 227 <option value="manual">manually setting them for each selected input</option>
221 </param> 228 </param>
245 </when> 252 </when>
246 </conditional> 253 </conditional>
247 <param name="project_name" type="text" value="myProject" label="Project name" help="Outputs will have this base name"> 254 <param name="project_name" type="text" value="myProject" label="Project name" help="Outputs will have this base name">
248 <validator type="empty_field"/> 255 <validator type="empty_field"/>
249 </param> 256 </param>
250 <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/> 257 <param name="rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/>
251 <conditional name="specify_genomic_window_cond"> 258 <conditional name="specify_genomic_window_cond">
252 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data"> 259 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
253 <option value="no" selected="true">No</option> 260 <option value="no" selected="true">No</option>
254 <option value="yes">Yes</option> 261 <option value="yes">Yes</option>
255 </param> 262 </param>
270 </when> 277 </when>
271 <when value="yes"> 278 <when value="yes">
272 <param name="bed_input" type="data" format="bed" label="Bed file specifying the genomic windows"/> 279 <param name="bed_input" type="data" format="bed" label="Bed file specifying the genomic windows"/>
273 </when> 280 </when>
274 </conditional> 281 </conditional>
275 <param argument="-bychr" type="boolean" truevalue="-bychr" falsevalue="" checked="False" label="Output chromosomes in separate files"/> 282 <param name="bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
276 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each genomic window using"> 283 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each genomic window using">
277 <option value="6" selected="true">mean</option> 284 <option value="6" selected="true">mean</option>
278 <option value="8">max</option> 285 <option value="8">max</option>
279 </param> 286 </param>
280 <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/> 287 <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
281 <param argument="-norm" type="boolean" truevalue="-norm" falsevalue="" checked="False" label="Standardize all datasets"/> 288 <param name="norm" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
282 <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/> 289 <param name="hp" type="boolean" truevalue="true" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/>
283 <param name="log2" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero means no log2 transformation"/> 290 <param name="log2" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero means no log2 transformation"/>
284 <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"/> 291 <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"/>
285 <param name="initial_states" type="integer" value="20" min="0" label="Initial number of states" help="Positive integer"/> 292 <param name="initial_states" type="integer" value="20" min="0" label="Initial number of states" help="Positive integer"/>
286 <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"/> 293 <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"/>
287 <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"/> 294 <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"/>
289 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/> 296 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/>
290 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/> 297 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/>
291 <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"/> 298 <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"/>
292 <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"/> 299 <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"/>
293 <param name="output_heatmaps" type="select" display="radio" label="Output heatmaps?"> 300 <param name="output_heatmaps" type="select" display="radio" label="Output heatmaps?">
294 <option value="no" selected="true">No</option> 301 <option value="yes" selected="true">Yes</option>
295 <option value="yes">Yes</option> 302 <option value="no">No</option>
296 </param> 303 </param>
297 <param name="save_ideas_log" type="select" display="radio" label="Save IDEAS log in an additional history item"> 304 <param name="save_ideas_log" type="select" display="radio" label="Save IDEAS log in an additional history item">
298 <option value="no" selected="true">No</option> 305 <option value="no" selected="true">No</option>
299 <option value="yes">Yes</option> 306 <option value="yes">Yes</option>
300 </param> 307 </param>