Mercurial > repos > nml > filter_density
comparison filter-density.xml @ 0:c27b4346352f draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
| author | nml |
|---|---|
| date | Tue, 27 Aug 2019 12:30:47 -0400 |
| parents | |
| children | c9a43abcd993 |
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| -1:000000000000 | 0:c27b4346352f |
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| 1 <tool id="filterdensity" name="Filter Density" version ="1.8.2"> | |
| 2 <description>Identify high density positions within indvidual genomes</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"> | |
| 7 bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out | |
| 8 #if $window_size: | |
| 9 --window_size $window_size | |
| 10 #end if | |
| 11 #if $threshold: | |
| 12 --threshold $threshold | |
| 13 #end if | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param name="vcf" type="data" label="Input vcf file" format="vcf" /> | |
| 17 <param name="window_size" type="integer" label="Size of search window" format="" optional="true"/> | |
| 18 <param name="threshold" type="integer" label="Density threshold cutoff" format="" optional="true"/> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="txt" name="out" label="High density regions"/> | |
| 22 <data format="bcf" name="filtered_bcf"/> | |
| 23 </outputs> | |
| 24 <tests> | |
| 25 <test> | |
| 26 <param name="threshold" value="2"/> | |
| 27 <param name="window_size" value="100"/> | |
| 28 <param name="vcf" value="1.vcf"/> | |
| 29 <output name="out" file="density_regions.txt"/> | |
| 30 </test> | |
| 31 </tests> | |
| 32 | |
| 33 <help> | |
| 34 What it does | |
| 35 ============ | |
| 36 | |
| 37 This script will indentify all high density SNV regions in an isolate genome, marking them as filtered-density in the associated bcf, if desired. | |
| 38 | |
| 39 | |
| 40 Usage | |
| 41 ===== | |
| 42 | |
| 43 **Parameters** | |
| 44 - vcf - A vcf file to be analyzed for SNV density. | |
| 45 - threshold - The threshold distance between SNV's in order for them to be considered 'high density' | |
| 46 - window_size - The size of the window, in base pairs, that will be looked at at any given time to calculate density. | |
| 47 </help> | |
| 48 | |
| 49 <citations> | |
| 50 </citations> | |
| 51 | |
| 52 </tool> |