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comparison ideas.xml @ 120:cfa683d96cae draft

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author greg
date Fri, 17 Nov 2017 13:13:27 -0500
parents 1d99221369b1
children e2995f2f127f
comparison
equal deleted inserted replaced
119:1d99221369b1 120:cfa683d96cae
7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement> 7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
8 <requirement type="package" version="1.20">ideas</requirement> 8 <requirement type="package" version="1.20">ideas</requirement>
9 <requirement type="package" version="1.4.4">r-optparse</requirement> 9 <requirement type="package" version="1.4.4">r-optparse</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #set output_dir = "output_dir" 12 #set output_pdf_dir = "output_pdf_dir"
13 #set output_txt_dir = "output_txt_dir"
13 #set tmp_dir = "tmp" 14 #set tmp_dir = "tmp"
14 #set prep_input_config = "prep_input_config.txt" 15 #set prep_input_config = "prep_input_config.txt"
15 #set prep_output_config = "prep_output_config.txt" 16 #set prep_output_config = "prep_output_config.txt"
16 ############################################## 17 ##############################################
17 ## Create the config file and prepare the data 18 ## Create the config file and prepare the data
18 ############################################## 19 ##############################################
19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 20 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
20 mkdir '$output_dir' && 21 mkdir '$output_pdf_dir' &&
22 mkdir '$output_txt_dir' &&
21 cp '$gen_prep_input_config' $prep_input_config && 23 cp '$gen_prep_input_config' $prep_input_config &&
22 prepMat 24 prepMat
23 $prep_input_config 25 $prep_input_config
24 #if str($specify_genomic_window) == "yes": 26 #if str($specify_genomic_window) == "yes":
25 -bed '$specify_genomic_window_cond.bed_input' 27 -bed '$specify_genomic_window_cond.bed_input'
92 #if str($save_ideas_log) == "yes": 94 #if str($save_ideas_log) == "yes":
93 > $output_log 95 > $output_log
94 #else: 96 #else:
95 > /dev/null 97 > /dev/null
96 #end if 98 #end if
97 && mv ./*.cluster '$output_dir' 99 && mv ./*.cluster '$output_txt_dir'
98 && mv ./*.para '$output_dir' 100 && mv ./*.para '$output_txt_dir'
99 && mv ./*.profile '$output_dir' 101 && mv ./*.profile '$output_txt_dir'
100 && mv ./*.state '$output_dir' 102 && mv ./*.state '$output_txt_dir'
101 && Rscript '$__tool_directory__/create_heatmap.R' 103 && Rscript '$__tool_directory__/create_heatmap.R'
102 -i '$output_dir/myProject.para' 104 -i '$output_txt_dir'
103 -o '$output_heatmap' 105 -o '$output_pdf_dir'
104 ]]></command> 106 ]]></command>
105 <configfiles> 107 <configfiles>
106 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 108 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
107 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 109 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
108 #for $i in $cell_type_epigenetic_factor_cond.input: 110 #for $i in $cell_type_epigenetic_factor_cond.input:
208 </inputs> 210 </inputs>
209 <outputs> 211 <outputs>
210 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}"> 212 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
211 <filter>save_ideas_log == 'yes'</filter> 213 <filter>save_ideas_log == 'yes'</filter>
212 </data> 214 </data>
213 <data name="output_heatmap" format="pdf" label="${tool.name} (heatmap) on ${on_string}"/> 215 <collection name="output_pdf_collection" type="list">
216 <discover_datasets pattern="__name__" directory="output_pdf_dir" format="pdf"/>
217 </collection>
214 <collection name="output_txt_collection" type="list"> 218 <collection name="output_txt_collection" type="list">
215 <discover_datasets pattern="__name__" directory="output_dir" format="txt"/> 219 <discover_datasets pattern="__name__" directory="output_txt_dir" format="txt"/>
216 </collection> 220 </collection>
217 </outputs> 221 </outputs>
218 <tests> 222 <tests>
219 <test> 223 <test>
220 <param name="cell_type_epigenetic_factor" value="extract"/> 224 <param name="cell_type_epigenetic_factor" value="extract"/>
223 <param name="specify_genomic_window" value="yes"/> 227 <param name="specify_genomic_window" value="yes"/>
224 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/> 228 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
225 <param name="project_name" value="IDEAS_out"/> 229 <param name="project_name" value="IDEAS_out"/>
226 <output_collection name="output_txt_collection" type="list"> 230 <output_collection name="output_txt_collection" type="list">
227 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/> 231 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
228 <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/> 232 <element name="IDEAS_out.para" file="IDEAS_out.para" ftype="txt"/>
229 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/> 233 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
230 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/> 234 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
231 </output_collection> 235 </output_collection>
232 <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/> 236 <output_collection name="output_pdf_collection" type="list">
237 <element name="something.pdf" file="IDEAS_out.cluster" compare="contains"/>
238 </output_collection>
233 </test> 239 </test>
234 <test> 240 <test>
235 <param name="cell_type_epigenetic_factor" value="manual"/> 241 <param name="cell_type_epigenetic_factor" value="manual"/>
236 <repeat name="input_repeat"> 242 <repeat name="input_repeat">
237 <param name="cell_type_name" value="e001" /> 243 <param name="cell_type_name" value="e001" />
241 <param name="specify_genomic_window" value="yes"/> 247 <param name="specify_genomic_window" value="yes"/>
242 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/> 248 <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
243 <param name="project_name" value="IDEAS_out"/> 249 <param name="project_name" value="IDEAS_out"/>
244 <output_collection name="output_txt_collection" type="list"> 250 <output_collection name="output_txt_collection" type="list">
245 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/> 251 <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
246 <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/> 252 <element name="IDEAS_out.para" file="IDEAS_out.para" ftype="txt"/>
247 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/> 253 <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
248 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/> 254 <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
249 </output_collection> 255 </output_collection>
250 <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/> 256 <output_collection name="output_pdf_collection" type="list">
257 <element name="something.pdf" file="IDEAS_out.cluster" compare="contains"/>
258 </output_collection>
251 </test> 259 </test>
252 </tests> 260 </tests>
253 <help> 261 <help>
254 **What it does** 262 **What it does**
255 263