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comparison ideas_preprocessor.xml @ 13:4d542da396a7 draft

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Uploaded
author greg
date Wed, 24 Jan 2018 14:04:47 -0500
parents 26eb979cf8d9
children aaf64c0d7a0e
comparison
equal deleted inserted replaced
12:ab0f306504a3 13:4d542da396a7
43 $chroms.append($i) 43 $chroms.append($i)
44 #end for 44 #end for
45 --restrict_to_chroms ",".join(chroms) 45 --restrict_to_chroms ",".join(chroms)
46 #end if 46 #end if
47 #end if 47 #end if
48 #if str($bychr) == "true":
49 --bychr true
50 #end if
48 --reads_per_bp $reads_per_bp 51 --reads_per_bp $reads_per_bp
49 #if str($exclude_input) not in ["None", ""]: 52 #if str($exclude_bed_input) not in ["None", ""]:
50 --exclude_input '$exclude_input' 53 --exclude_bed_input '$exclude_bed_input'
54 #end if
55 #if str($standardize_datasets) == "true":
56 --standardize_datasets true
51 #end if 57 #end if
52 --output '$output' 58 --output '$output'
53 --output_hid $output.hid 59 --output_hid $output.hid
54 --output_files_path '$output.files_path' 60 --output_files_path '$output.files_path'
55 &> ideas_preprocessor_log.txt; 61 &> ideas_preprocessor_log.txt;
154 </repeat> 160 </repeat>
155 </when> 161 </when>
156 </conditional> 162 </conditional>
157 </when> 163 </when>
158 <when value="yes"> 164 <when value="yes">
159 <param name="chrom_bed_input" type="data" format="bed" label="Bed file for defining the chromosome window positions"> 165 <param name="chrom_bed_input" type="data" format="bed" label="Select bed file for defining chromosome window positions">
160 <validator type="empty_dataset"/> 166 <validator type="empty_dataset"/>
161 </param> 167 </param>
162 </when> 168 </when>
163 </conditional> 169 </conditional>
164 <param name="bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/> 170 <param name="bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
165 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each window using"> 171 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each window using">
166 <option value="6" selected="true">mean</option> 172 <option value="6" selected="true">mean</option>
167 <option value="8">max</option> 173 <option value="8">max</option>
168 </param> 174 </param>
169 <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/> 175 <param name="exclude_bed_input" type="data" format="bed" optional="True" multiple="True" label="Select bed file(s) containing regions to exclude"/>
170 <param name="standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/> 176 <param name="standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
171 </inputs> 177 </inputs>
172 <outputs> 178 <outputs>
173 <data name="output" format="ideaspre"/> 179 <data name="output" format="ideaspre"/>
174 </outputs> 180 </outputs>