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comparison ideas.xml @ 165:bb5544d1c85e draft

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author greg
date Thu, 18 Jan 2018 13:47:35 -0500
parents 68d909206a15
children 5c5e2f7b34c8
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164:68d909206a15 165:bb5544d1c85e
15 #set output_training_dir = "output_training_dir" 15 #set output_training_dir = "output_training_dir"
16 #set tmp_dir = "tmp" 16 #set tmp_dir = "tmp"
17 #set prep_input_config = "prep_input_config.txt" 17 #set prep_input_config = "prep_input_config.txt"
18 #set prep_output_config = "prep_output_config.txt" 18 #set prep_output_config = "prep_output_config.txt"
19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
20 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
20 #set perform_training = $perform_training_cond.perform_training 21 #set perform_training = $perform_training_cond.perform_training
21 ############################################## 22 ##############################################
22 ## Create the config file and prepare the data 23 ## Create the config file and prepare the data
23 ############################################## 24 ##############################################
24 #if str($output_heatmaps) == "yes": 25 #if str($output_heatmaps) == "yes":
25 mkdir '$output_pdf_dir' && 26 mkdir '$output_pdf_dir' &&
26 #end if 27 #end if
27 #if str($perform_training) == "yes": 28 #if str($perform_training) == "yes":
29 #set output_dir = $output_training_dir
28 mkdir '$output_training_dir' && 30 mkdir '$output_training_dir' &&
29 #end if 31 #else:
30 mkdir '$output_txt_dir' && 32 #set output_dir = $output_txt_dir
33 mkdir '$output_txt_dir' &&
34 #end if
31 cp '$gen_prep_input_config' $prep_input_config && 35 cp '$gen_prep_input_config' $prep_input_config &&
32 sort $prep_input_config -o $prep_input_config && 36 sort $prep_input_config -o $prep_input_config &&
33 prepMat 37 prepMat
34 $prep_input_config 38 $prep_input_config
35 #if str($specify_genomic_window) == "yes": 39 #if str($specify_genomic_window) == "yes":
53 -exclude '$blacklist_input' 57 -exclude '$blacklist_input'
54 #end if 58 #end if
55 $norm 59 $norm
56 &>prepmat_log.txt; 60 &>prepmat_log.txt;
57 if [[ $? -ne 0 ]]; then 61 if [[ $? -ne 0 ]]; then
58 cp prepmat_log.txt '$output_txt_dir'; 62 cp prepmat_log.txt '$output_dir';
59 exit 1; 63 exit 1;
60 fi 64 fi
61 ############################################## 65 ##############################################
62 ## Coerce the prepMat config output to the 66 ## Coerce the prepMat config output to the
63 ## format expected by IDEAS. 67 ## format expected by IDEAS.
69 ############################################## 73 ##############################################
70 ## Using a genomic window bed file, so categorize 74 ## Using a genomic window bed file, so categorize
71 ## the window positions by chromosome to enable 75 ## the window positions by chromosome to enable
72 ## the IDEAS -inv option. 76 ## the IDEAS -inv option.
73 ############################################## 77 ##############################################
74 #import collections 78 && cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config
75 #set window_positions_by_chroms = collections.OrderedDict() 79 #end if
76 #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')): 80 && Rscript '$__tool_directory__/ideas.R'
77 #set $line = $line.strip() 81 #if str($specify_genomic_window) == "yes":
78 #if not $line or $line.startswith('#'): 82 --windows_bed '$specify_genomic_window_cond.bed_input'
79 #continue 83 --windows_config $windows_positions_by_chroms_config
80 #end if 84 #end if
81 #set items = $line.split('\t') 85 #if str($perform_training) == "yes":
82 #if $items[0] in $window_positions_by_chroms: 86 --training_iterations $perform_training_cond.training_iterations
83 #set tup = $window_positions_by_chroms[$items[0]] 87 --training_windows $perform_training_cond.training_windows
84 #set $tup[1] += 1 88 #end if
85 #set $window_positions_by_chroms[$items[0]] = $tup 89 --prep_output_config '$prep_output_config'
86 #else: 90 --hp $hp
87 #set $window_positions_by_chroms[$items[0]] = [$count, $count+1] 91 #if str($log2) != "0.0":
88 #end if 92 --log2 $log2
89 #end for 93 #end if
90 #for chrom, tup in $window_positions_by_chroms.items(): 94 #if str($max_states) != "0.0":
91 && Rscript '$__tool_directory__/ideas.R' 95 --max_states $max_states
92 #if str($perform_training) == "yes": 96 #end if
93 --training_iterations $perform_training_cond.training_iterations 97 #if str($initial_states) != "0":
94 --training_windows $perform_training_cond.training_windows 98 --initial_states $initial_states
95 #end if 99 #end if
96 --prep_output_config '$prep_output_config' 100 #if str($max_position_classes) != "0":
97 --windows_bed '$specify_genomic_window_cond.bed_input' 101 --max_position_classes $max_position_classes
98 --hp $hp 102 #end if
99 --window_start $tup[0] 103 #if str($max_cell_type_clusters) != "0":
100 --window_end $tup[1] 104 --max_cell_type_clusters $max_cell_type_clusters
101 #if str($log2) != "0.0": 105 #end if
102 --log2 $log2 106 #if str($prior_concentration) != "0.0":
103 #end if 107 --prior_concentration $prior_concentration
104 #if str($max_states) != "0.0": 108 #end if
105 --max_states $max_states 109 --burnin_num $burnin_num
106 #end if 110 --mcmc_num $mcmc_num
107 #if str($initial_states) != "0": 111 #if str($minerr) != "0.0":
108 --initial_states $initial_states 112 --minerr $minerr
109 #end if 113 #end if
110 #if str($max_position_classes) != "0": 114 #if str($maxerr) != "0.0":
111 --max_position_classes $max_position_classes 115 --maxerr $maxerr
112 #end if 116 #end if
113 #if str($max_cell_type_clusters) != "0": 117 --rseed $rseed
114 --max_cell_type_clusters $max_cell_type_clusters 118 --thread \${GALAXY_SLOTS:-4}
115 #end if 119 --project_name '$project_name'
116 #if str($prior_concentration) != "0.0": 120 #if str($save_ideas_log) == "yes":
117 --prior_concentration $prior_concentration 121 --save_ideas_log $save_ideas_log
118 #end if 122 --output_log '$output_log'
119 --burnin_num $burnin_num 123 #end if
120 --mcmc_num $mcmc_num 124 #if str($perform_training) == "yes":
121 #if str($minerr) != "0.0": 125 && mv ./*.para0 '$output_dir'
122 --minerr $minerr 126 && mv ./*.profile0 '$output_dir'
123 #end if
124 #if str($maxerr) != "0.0":
125 --maxerr $maxerr
126 #end if
127 --rseed $rseed
128 --thread \${GALAXY_SLOTS:-4}
129 --project_name '$project_name.$chrom'
130 #if str($save_ideas_log) == "yes":
131 --save_ideas_log $save_ideas_log
132 --output_log '$output_log'
133 #end if
134 #end for
135 #else: 127 #else:
136 ############################################## 128 && mv ./*.para '$output_dir'
137 ## Not using a genomic window bed file. 129 && mv ./*.profile '$output_dir'
138 ############################################## 130 #end if
139 && Rscript '$__tool_directory__/ideas.R' 131 && mv ./*.cluster '$output_dir'
132 && mv ./*.state '$output_dir'
133 #if str($output_heatmaps) == "yes":
134 && Rscript '$__tool_directory__/create_heatmaps.R'
135 --input_dir '$output_dir'
136 --output_dir '$output_pdf_dir'
137 --script_dir '$__tool_directory__'
140 #if str($perform_training) == "yes": 138 #if str($perform_training) == "yes":
141 --training_iterations $perform_training_cond.training_iterations
142 --training_windows $perform_training_cond.training_windows
143 #end if
144 --prep_output_config '$prep_output_config'
145 --windows_bed $tmp_dir/*.bed
146 --hp $hp
147 #if str($log2) != "0.0":
148 --log2 $log2
149 #end if
150 #if str($max_states) != "0.0":
151 --max_states $max_states
152 #end if
153 #if str($initial_states) != "0":
154 --initial_states $initial_states
155 #end if
156 #if str($max_position_classes) != "0":
157 --max_position_classes $max_position_classes
158 #end if
159 #if str($max_cell_type_clusters) != "0":
160 --max_cell_type_clusters $max_cell_type_clusters
161 #end if
162 #if str($prior_concentration) != "0.0":
163 --prior_concentration $prior_concentration
164 #end if
165 --burnin_num $burnin_num
166 --mcmc_num $mcmc_num
167 #if str($minerr) != "0.0":
168 --minerr $minerr
169 #end if
170 #if str($maxerr) != "0.0":
171 --maxerr $maxerr
172 #end if
173 --rseed $rseed
174 --thread \${GALAXY_SLOTS:-4}
175 --project_name '$project_name'
176 #if str($save_ideas_log) == "yes":
177 --save_ideas_log $save_ideas_log
178 --output_log '$output_log'
179 #end if
180 #end if
181 #if str($perform_training) == "yes":
182 && mv ./*.para0 '$output_training_dir'
183 && mv ./*.profile0 '$output_training_dir'
184 #if str($output_heatmaps) == "yes":
185 && Rscript '$__tool_directory__/create_heatmaps.R'
186 --input_dir 'output_training_dir'
187 --output_dir '$output_pdf_dir'
188 --script_dir '$__tool_directory__'
189 --in_training_mode true 139 --in_training_mode true
190 #end if
191 #else:
192 && mv ./*.cluster '$output_txt_dir'
193 && mv ./*.para '$output_txt_dir'
194 && mv ./*.profile '$output_txt_dir'
195 && mv ./*.state '$output_txt_dir'
196 #if str($output_heatmaps) == "yes":
197 && Rscript '$__tool_directory__/create_heatmaps.R'
198 --input_dir '$output_txt_dir'
199 --output_dir '$output_pdf_dir'
200 --script_dir '$__tool_directory__'
201 #end if 140 #end if
202 #end if 141 #end if
203 ]]></command> 142 ]]></command>
204 <configfiles> 143 <configfiles>
205 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 144 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
223 #else: 162 #else:
224 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat: 163 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
225 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 164 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
226 #end for 165 #end for
227 #end if]]></configfile> 166 #end if]]></configfile>
167 <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes":
168 #import collections
169 #set window_positions_by_chroms_odict = $collections.OrderedDict()
170 #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
171 #set $line = $line.strip()
172 #if not $line or $line.startswith('#'):
173 #continue
174 #end if
175 #set items = $line.split('\t')
176 #if $items[0] in $window_positions_by_chroms_odict:
177 #set tup = $window_positions_by_chroms_odict[$items[0]]
178 #set $tup[1] += 1
179 #set $window_positions_by_chroms_odict[$items[0]] = $tup
180 #else:
181 #set $window_positions_by_chroms_odict[$items[0]] = [$count, $count+1]
182 #end if
183 #end for
184 #for $chrom, $tup in $window_positions_by_chroms_odict.items():
185 ${chrom} ${tup[0]} ${tup[1]}
186 #end for
187 #end if]]></configfile>
228 </configfiles> 188 </configfiles>
229 <inputs> 189 <inputs>
230 <conditional name="perform_training_cond"> 190 <conditional name="perform_training_cond">
231 <param name="perform_training" type="select" label="Perform training?"> 191 <param name="perform_training" type="select" label="Perform training?">
232 <option value="yes" selected="true">Yes</option> 192 <option value="yes" selected="true">Yes</option>
233 <option value="no">No</option> 193 <option value="no">No</option>
234 </param> 194 </param>
235 <when value="yes"> 195 <when value="yes">
236 <param name="training_iterations" type="integer" value="20" min="2" label="Number of training iterations"/> 196 <param name="training_iterations" type="integer" value="20" min="3" label="Number of training iterations"/>
237 <param name="training_windows" type="integer" value="10000" min="2" label="Number of randomly selected windows for training"/> 197 <param name="training_windows" type="integer" value="10000" min="2" label="Number of randomly selected windows for training"/>
238 </when> 198 </when>
239 <when value="no"/> 199 <when value="no"/>
240 </conditional> 200 </conditional>
241 <conditional name="cell_type_epigenetic_factor_cond"> 201 <conditional name="cell_type_epigenetic_factor_cond">