Mercurial > repos > greg > ideas_preprocessor

comparison ideas_preprocessor.xml @ 22:3651f1592f3f draft

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author greg
date Wed, 31 Jan 2018 14:13:11 -0500
parents 237ee7319452
children 71345e154c66
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21:99102499271a 22:3651f1592f3f
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #set chromosome_windows = "chromosome_windows.txt" 11 #set chromosome_windows = "chromosome_windows.txt"
12 #set ideaspre_input_config = "ideaspre_input_config.txt" 12 #set ideaspre_input_config = "ideaspre_input_config.txt"
13 #set specify_chrom_windows = $specify_chrom_windows_cond.specify_chrom_windows 13 #set specify_chrom_windows = $specify_chrom_windows_cond.specify_chrom_windows
14 #set tmp_dir = "tmp"
15 mkdir $tmp_dir &&
14 mkdir $output.files_path && 16 mkdir $output.files_path &&
15 #if str($specify_chrom_windows) == "yes": 17 #if str($specify_chrom_windows) == "yes":
16 ############################################## 18 ##############################################
17 ## Using a bed file for defining chrom windows, 19 ## Using a bed file for defining chrom windows,
18 ## so categorize the window positions by 20 ## so categorize the window positions by
177 </outputs> 179 </outputs>
178 <tests> 180 <tests>
179 <test> 181 <test>
180 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/> 182 <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
181 <param name="specify_chrom_windows" value="yes"/> 183 <param name="specify_chrom_windows" value="yes"/>
182 <param name="chrom_bed_input" value="chrom_windows.bed" ftype="bed" dbkey="hg19"/> 184 <param name="chrom_bed_input" value="chromosomes.bed" ftype="bed" dbkey="hg19"/>
183 <output name="output" file="output.ideaspre" ftype="ideaspre" /> 185 <output name="output" file="output.html" ftype="ideaspre">
186 <extra_files type="file" name="chromosomes.bed" value="chromosomes.bed"/>
187 <extra_files type="file" name="chromosome_windows.txt" value="chromosome_windows.txt"/>
188 <extra_files type="file" name="IDEAS_input_config.txt" value="IDEAS_input_config.txt"/>
189 <extra_files type="file" name="tmp.tar" value="tmp.tar" compare="sim_size"/>
190 </output>
184 </test> 191 </test>
185 </tests> 192 </tests>
186 <help> 193 <help>
187 **What it does** 194 **What it does**
188 195