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comparison ideas.xml @ 131:5150fcdcd0fa draft

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Uploaded
author greg
date Tue, 12 Dec 2017 10:13:26 -0500
parents d088f25661d9
children 8ce93420010c
comparison
equal deleted inserted replaced
130:d088f25661d9 131:5150fcdcd0fa
42 -c $reads_per_bp 42 -c $reads_per_bp
43 #if str($blacklist_input) not in ["None", ""]: 43 #if str($blacklist_input) not in ["None", ""]:
44 -exclude '$blacklist_input' 44 -exclude '$blacklist_input'
45 #end if 45 #end if
46 $norm 46 $norm
47 &>prepmat.log;
48 if [[ $? -ne 0 ]]; then
49 cp prepmat.log '$output_txt_dir';
50 exit 1;
51 fi
47 ############################################## 52 ##############################################
48 ## Coerce the prepMat config output to the 53 ## Coerce the prepMat config output to the
49 ## format expected by IDEAS. 54 ## format expected by IDEAS.
50 ############################################## 55 ##############################################
51 && cut -d' ' $prep_input_config -f1,2 > file1.txt 56 && cut -d' ' $prep_input_config -f1,2 > file1.txt
106 #end if 111 #end if
107 -rseed $rseed 112 -rseed $rseed
108 -thread \${GALAXY_SLOTS:-4} 113 -thread \${GALAXY_SLOTS:-4}
109 -o '$project_name.$chrom' 114 -o '$project_name.$chrom'
110 #if str($save_ideas_log) == "yes": 115 #if str($save_ideas_log) == "yes":
111 >> $output_log 116 &>>'$output_log';
117 if [[ $? -ne 0 ]]; then
118 exit 1;
119 fi
112 #else: 120 #else:
113 > /dev/null 121 &>>ideas_log.txt;
114 #end if 122 if [[ $? -ne 0 ]]; then
123 cp ideas_log.txt '$output_txt_dir'
124 exit 1;
125 fi
126 #end if
127
115 #end for 128 #end for
116 #else: 129 #else:
117 && ideas 130 && ideas
118 '$prep_output_config' 131 '$prep_output_config'
119 $tmp_dir/*.bed 132 $tmp_dir/*.bed
145 #end if 158 #end if
146 -rseed $rseed 159 -rseed $rseed
147 -thread \${GALAXY_SLOTS:-4} 160 -thread \${GALAXY_SLOTS:-4}
148 -o '$project_name' 161 -o '$project_name'
149 #if str($save_ideas_log) == "yes": 162 #if str($save_ideas_log) == "yes":
150 > $output_log 163 &>'$output_log';
164 if [[ $? -ne 0 ]]; then
165 exit 1;
166 fi
151 #else: 167 #else:
152 > /dev/null 168 &>ideas_log.txt;
169 if [[ $? -ne 0 ]]; then
170 cp ideas_log.txt '$output_txt_dir'
171 exit 1;
172 fi
153 #end if 173 #end if
154 #end if 174 #end if
155 && mv ./*.cluster '$output_txt_dir' 175 && mv ./*.cluster '$output_txt_dir'
156 && mv ./*.para '$output_txt_dir' 176 && mv ./*.para '$output_txt_dir'
157 && mv ./*.profile '$output_txt_dir' 177 && mv ./*.profile '$output_txt_dir'
158 && mv ./*.state '$output_txt_dir' 178 && mv ./*.state '$output_txt_dir'
159 && Rscript '$__tool_directory__/create_heatmap.R' 179 #if str($output_heatmaps) == "yes":
160 -i '$output_txt_dir' 180 && Rscript '$__tool_directory__/create_heatmap.R'
161 -o '$output_pdf_dir' 181 -i '$output_txt_dir'
182 -o '$output_pdf_dir'
183 #end if
162 ]]></command> 184 ]]></command>
163 <configfiles> 185 <configfiles>
164 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 186 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
165 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 187 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
166 #for $i in $cell_type_epigenetic_factor_cond.input: 188 #for $i in $cell_type_epigenetic_factor_cond.input:
260 <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default: sqrt(number of cell types)"/> 282 <param name="prior_concentration" type="float" value="1" min="0" label="Prior concentration" help="Zero value results in the default: sqrt(number of cell types)"/>
261 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/> 283 <param name="burnin_num" type="integer" value="20" min="1" label="Number of burnin steps"/>
262 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/> 284 <param name="mcmc_num" type="integer" value="20" min="1" label="Number of maximization steps"/>
263 <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"/> 285 <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"/>
264 <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"/> 286 <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"/>
287 <param name="output_heatmaps" type="select" display="radio" label="Output heatmaps?">
288 <option value="no" selected="true">No</option>
289 <option value="yes">Yes</option>
290 </param>
265 <param name="save_ideas_log" type="select" display="radio" label="Save IDEAS log in an additional history item"> 291 <param name="save_ideas_log" type="select" display="radio" label="Save IDEAS log in an additional history item">
266 <option value="no" selected="true">No</option> 292 <option value="no" selected="true">No</option>
267 <option value="yes">Yes</option> 293 <option value="yes">Yes</option>
268 </param> 294 </param>
269 </inputs> 295 </inputs>
270 <outputs> 296 <outputs>
271 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}"> 297 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
272 <filter>save_ideas_log == 'yes'</filter> 298 <filter>save_ideas_log == 'yes'</filter>
273 </data> 299 </data>
274 <collection name="output_pdf_collection" type="list" label="${tool.name} (heatmaps on ${on_string}"> 300 <collection name="output_pdf_collection" type="list" label="${tool.name} (heatmaps) on ${on_string}">
275 <discover_datasets pattern="__name__" directory="output_pdf_dir" format="pdf"/> 301 <discover_datasets pattern="__name__" directory="output_pdf_dir" format="pdf"/>
302 <filter>output_heatmaps == 'yes'</filter>
276 </collection> 303 </collection>
277 <collection name="output_txt_collection" type="list"> 304 <collection name="output_txt_collection" type="list">
278 <discover_datasets pattern="__name__" directory="output_txt_dir" format="txt"/> 305 <discover_datasets pattern="__name__" directory="output_txt_dir" format="txt"/>
279 </collection> 306 </collection>
280 </outputs> 307 </outputs>