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comparison ideas_preprocessor.xml @ 26:06e63b5cb025 draft

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author greg
date Mon, 05 Feb 2018 13:42:03 -0500
parents 71345e154c66
children 55d264cd49e8
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25:f7563bb242fc 26:06e63b5cb025
33 --chromosome_windows '$chromosome_windows' 33 --chromosome_windows '$chromosome_windows'
34 --chrom_bed_input '$specify_chrom_windows_cond.chrom_bed_input' 34 --chrom_bed_input '$specify_chrom_windows_cond.chrom_bed_input'
35 #else: 35 #else:
36 --chrom_len_file '$chromInfo' 36 --chrom_len_file '$chromInfo'
37 --window_size $specify_chrom_windows_cond.window_size 37 --window_size $specify_chrom_windows_cond.window_size
38 #set restrict_chromosomes = $specify_chrom_windows_cond.restrict_chromosomes_cond.restrict_chromosomes
39 #if str($restrict_chromosomes) == "yes":
40 #set chroms = []
41 #set chrom_repeat = $specify_chrom_windows_cond.restrict_chromosomes_cond.chrom_repeat
42 #for $i in $chrom_repeat.chrom
43 $chroms.append($i)
44 #end for
45 --restrict_to_chroms ",".join(chroms)
46 #end if
47 #end if 38 #end if
48 #if str($bychr) == "true":
49 --bychr true
50 #end if
51 --reads_per_bp $reads_per_bp
52 #if str($exclude_bed_input) not in ["None", ""]: 39 #if str($exclude_bed_input) not in ["None", ""]:
53 --exclude_bed_input '$exclude_bed_input' 40 #set exclude_bed_inputs = list()
54 #end if 41 #for $i in $exclude_bed_input:
55 #if str($standardize_datasets) == "true": 42 $exclude_bed_input.append(str($i))
56 --standardize_datasets true 43 #end for
44 #set exclude_bed_inputs = ",".join($exclude_bed_inputs)
45 --exclude_bed_input '$exclude_bed_inputs'
57 #end if 46 #end if
58 --output '$output' 47 --output '$output'
59 --output_files_path '$output.files_path' 48 --output_files_path '$output.files_path'
60 &> ideas_preprocessor_log.txt; 49 &> ideas_preprocessor_log.txt;
61 if [[ $? -ne 0 ]]; then 50 if [[ $? -ne 0 ]]; then
145 <option value="no" selected="true">No</option> 134 <option value="no" selected="true">No</option>
146 <option value="yes">Yes</option> 135 <option value="yes">Yes</option>
147 </param> 136 </param>
148 <when value="no"> 137 <when value="no">
149 <param name="window_size" type="integer" value="200" label="Window size in base pairs"/> 138 <param name="window_size" type="integer" value="200" label="Window size in base pairs"/>
150 <conditional name="restrict_chromosomes_cond">
151 <param name="restrict_chromosomes" type="select" label="Restrict processing to specified chromosomes">
152 <option value="no" selected="true">No</option>
153 <option value="yes">Yes</option>
154 </param>
155 <when value="no"/>
156 <when value="yes">
157 <repeat name="chrom_repeat" title="Chromosomes" min="1">
158 <param name="chrom" type="text" value="" label="Chromosome" help="One chromosome (e.g., chr1, chr2, chrX) per text field"/>
159 </repeat>
160 </when>
161 </conditional>
162 </when> 139 </when>
163 <when value="yes"> 140 <when value="yes">
164 <param name="chrom_bed_input" type="data" format="bed" label="Select bed file for defining chromosome window positions"> 141 <param name="chrom_bed_input" type="data" format="bed" label="Select bed file for defining chromosome window positions">
165 <validator type="empty_dataset"/> 142 <validator type="empty_dataset"/>
166 </param> 143 </param>
167 </when> 144 </when>
168 </conditional> 145 </conditional>
169 <param name="bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
170 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each window using">
171 <option value="6" selected="true">mean</option>
172 <option value="8">max</option>
173 </param>
174 <param name="exclude_bed_input" type="data" format="bed" optional="True" multiple="True" label="Select bed file(s) containing regions to exclude"/> 146 <param name="exclude_bed_input" type="data" format="bed" optional="True" multiple="True" label="Select bed file(s) containing regions to exclude"/>
175 <param name="standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
176 </inputs> 147 </inputs>
177 <outputs> 148 <outputs>
178 <data name="output" format="ideaspre"/> 149 <data name="output" format="ideaspre"/>
179 </outputs> 150 </outputs>
180 <tests> 151 <tests>
218 * **Selected input file name pattern is** - select the file name pattern, either **epigenetic factor name-cell type name** or **cell type name-epigenetic factor name**. 189 * **Selected input file name pattern is** - select the file name pattern, either **epigenetic factor name-cell type name** or **cell type name-epigenetic factor name**.
219 190
220 * **Define chromosome window positions from a bed file** - select "No" to run whole genome segmentation or select "Yes" to segment genomes within 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. 191 * **Define chromosome window positions from a bed file** - select "No" to run whole genome segmentation or select "Yes" to segment genomes within 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.
221 192
222 * **Window size in base pairs** - Window size in base pairs if specifying manually. 193 * **Window size in base pairs** - Window size in base pairs if specifying manually.
223 * **Restrict processing to specified chromosomes** - select "Yes" to restrict processing to specified chromosomes.
224
225 * **Chromosomes** - enter a comma-separated list of chromosomes for processing.
226
227 * **Select bed file for defining chromosome window positions** - select a bed file for specifying the chromosome window positions. 194 * **Select bed file for defining chromosome window positions** - select a bed file for specifying the chromosome window positions.
228 195
229 * **Output chromosomes in separate files** - select "Yes" to produce separate files for each chromosome, allowing you to run IDEAS on different chromosomes separately.
230 * **Calculate the signal in each window using** - use the bigWigAverageOverBed utility from the UCSC genome browser to calculate the signal (i.e., the number of reads per bp) in each window.
231 * **Select bed file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets. 196 * **Select bed file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets.
232 * **Standardize all datasets** - select "Yes" to standardize all datasets (e.g., reads / total_reads * 20 million) so that the signals from different cell types become comparable - your datasets can be read counts, logp-values or fold change.
233
234 </help> 197 </help>
235 <citations> 198 <citations>
236 <citation type="doi">10.1093/nar/gkw278</citation> 199 <citation type="doi">10.1093/nar/gkw278</citation>
237 </citations> 200 </citations>
238 </tool> 201 </tool>