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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
author nml
date Tue, 23 Jun 2020 10:25:36 -0400
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c9a43abcd993 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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1 <tool id="filterdensity" name="Filter Density" version ="@VERSION@+galaxy1">
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2 <description>Identify high density positions within indvidual genomes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out
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9 #if $window_size:
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10 --window_size $window_size
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11 #end if
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12 #if $threshold:
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13 --threshold $threshold
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14 #end if
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15 </command>
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16 <inputs>
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17 <param name="vcf" type="data" label="Input vcf file" format="vcf" />
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18 <param name="window_size" type="integer" min="1" label="Size of search window" format="" optional="true"/>
c9a43abcd993 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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19 <param name="threshold" type="integer" min="1" label="Density threshold cutoff" format="" optional="true"/>
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20 </inputs>
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21 <outputs>
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22 <data format="txt" name="out" label="High density regions"/>
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23 <data format="bcf" name="filtered_bcf"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="threshold" value="2"/>
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28 <param name="window_size" value="100"/>
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29 <param name="vcf" value="1.vcf"/>
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30 <output name="out" file="density_regions.txt"/>
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31 </test>
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32 </tests>
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34 <help>
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35 What it does
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36 ============
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38 This script will indentify all high density SNV regions in an isolate genome, marking them as filtered-density in the associated bcf, if desired.
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41 Usage
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42 =====
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44 **Parameters**
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45 - vcf - A vcf file to be analyzed for SNV density.
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46 - threshold - The threshold distance between SNV's in order for them to be considered 'high density'
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47 - window_size - The size of the window, in base pairs, that will be looked at at any given time to calculate density.
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48 </help>
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49 <expand macro="citations"/>
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50 </tool>