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comparison ideas.xml @ 108:021d1f60b0d3 draft

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author greg
date Wed, 15 Nov 2017 07:36:55 -0500
parents 278abbd4399c
children c47a3c6a01bd
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107:278abbd4399c 108:021d1f60b0d3
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_dir = "output_dir"
13 #set tmp_dir = "tmp" 13 #set tmp_dir = "tmp"
14 #set prep_input_config = "prep_input_config.txt" 14 #set prep_input_config = "prep_input_config.txt"
15 #set prep_output_config = "prep_output_config.txt" 15 #set prep_output_config = '$project_name'
16 ############################################## 16 ##############################################
17 ## Create the config file and prepare the data 17 ## Create the config file and prepare the data
18 ############################################## 18 ##############################################
19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
20 mkdir '$output_dir' && 20 mkdir '$output_dir' &&
152 <validator type="unspecified_build"/> 152 <validator type="unspecified_build"/>
153 </param> 153 </param>
154 </repeat> 154 </repeat>
155 </when> 155 </when>
156 </conditional> 156 </conditional>
157 <param name="project_name" type="text" value="" optional="false" label="Project name" help="Output datasets will have this base name"/>
157 <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."/> 158 <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."/>
158 <conditional name="specify_genomic_window_cond"> 159 <conditional name="specify_genomic_window_cond">
159 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data"> 160 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
160 <option value="no" selected="true">No</option> 161 <option value="no" selected="true">No</option>
161 <option value="yes">Yes</option> 162 <option value="yes">Yes</option>
288 289
289 * **Cell type name** - cell type name 290 * **Cell type name** - cell type name
290 * **Epigenetic factor name** - epigenetic factor name 291 * **Epigenetic factor name** - epigenetic factor name
291 * **BAM or BigWig file** - BAM or BigWig file 292 * **BAM or BigWig file** - BAM or BigWig file
292 293
294 * **Project name** - datasets produced by IDEAS will have this base name.
293 * **Seed for IDEAS model initialization** - enter an integer to be used as the seed for the IDEAS model initialization. A zero value causes IDEAS to automatically generate a random seed, and this seed will be different for each job run. 295 * **Seed for IDEAS model initialization** - enter an integer to be used as the seed for the IDEAS model initialization. A zero value causes IDEAS to automatically generate a random seed, and this seed will be different for each job run.
294 * **Select Bed file that defines genomic windows on which to process the data** - if "No" is selected, IDEAS will run whole genome segmentation. If "Yes" is selected, IDEAS will segment genomes in the unit of the windows defined by the bed file. This file can be in BED3, BED4 or BED5 format, but only the first three columns (chr posst posed) will be used. 296 * **Select Bed file that defines genomic windows on which to process the data** - if "No" is selected, IDEAS will run whole genome segmentation. If "Yes" is selected, IDEAS will segment genomes in the unit of the windows defined by the bed file. This file can be in BED3, BED4 or BED5 format, but only the first three columns (chr posst posed) will be used.
295 297
296 * **Window size in base pairs** - Window size in base pairs (if "No" is selected) 298 * **Window size in base pairs** - Window size in base pairs (if "No" is selected)
297 * **Restrict processing to specified chromosomes** - If "Yes" is selected, processing will be restricted to specified chromosomes 299 * **Restrict processing to specified chromosomes** - If "Yes" is selected, processing will be restricted to specified chromosomes