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annotate filter-density.xml @ 0:c27b4346352f draft

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