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comparison filter-density.xml @ 1:c9a43abcd993 draft default tip

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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
parents c27b4346352f
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0:c27b4346352f 1:c9a43abcd993
1 <tool id="filterdensity" name="Filter Density" version ="1.8.2"> 1 <tool id="filterdensity" name="Filter Density" version ="@VERSION@+galaxy1">
2 <description>Identify high density positions within indvidual genomes</description> 2 <description>Identify high density positions within indvidual genomes</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
7 bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out 8 bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out
8 #if $window_size: 9 #if $window_size:
9 --window_size $window_size 10 --window_size $window_size
10 #end if 11 #end if
12 --threshold $threshold 13 --threshold $threshold
13 #end if 14 #end if
14 </command> 15 </command>
15 <inputs> 16 <inputs>
16 <param name="vcf" type="data" label="Input vcf file" format="vcf" /> 17 <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="window_size" type="integer" min="1" label="Size of search window" format="" optional="true"/>
18 <param name="threshold" type="integer" label="Density threshold cutoff" format="" optional="true"/> 19 <param name="threshold" type="integer" min="1" label="Density threshold cutoff" format="" optional="true"/>
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <data format="txt" name="out" label="High density regions"/> 22 <data format="txt" name="out" label="High density regions"/>
22 <data format="bcf" name="filtered_bcf"/> 23 <data format="bcf" name="filtered_bcf"/>
23 </outputs> 24 </outputs>
43 **Parameters** 44 **Parameters**
44 - vcf - A vcf file to be analyzed for SNV density. 45 - 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 - 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 - 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 </help>
48 49 <expand macro="citations"/>
49 <citations>
50 </citations>
51
52 </tool> 50 </tool>