Mercurial > repos > nml > filter_density
changeset 1:c9a43abcd993 draft default tip
"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 |
| children | |
| files | filter-density.xml macros.xml |
| diffstat | 2 files changed, 24 insertions(+), 10 deletions(-) [+] |
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--- a/filter-density.xml Tue Aug 27 12:30:47 2019 -0400 +++ b/filter-density.xml Tue Jun 23 10:25:36 2020 -0400 @@ -1,8 +1,9 @@ -<tool id="filterdensity" name="Filter Density" version ="1.8.2"> +<tool id="filterdensity" name="Filter Density" version ="@VERSION@+galaxy1"> <description>Identify high density positions within indvidual genomes</description> - <requirements> - <requirement type="package" version="1.8.2">snvphyl-tools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"> bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out #if $window_size: @@ -14,8 +15,8 @@ </command> <inputs> <param name="vcf" type="data" label="Input vcf file" format="vcf" /> - <param name="window_size" type="integer" label="Size of search window" format="" optional="true"/> - <param name="threshold" type="integer" label="Density threshold cutoff" format="" optional="true"/> + <param name="window_size" type="integer" min="1" label="Size of search window" format="" optional="true"/> + <param name="threshold" type="integer" min="1" label="Density threshold cutoff" format="" optional="true"/> </inputs> <outputs> <data format="txt" name="out" label="High density regions"/> @@ -45,8 +46,5 @@ - threshold - The threshold distance between SNV's in order for them to be considered 'high density' - window_size - The size of the window, in base pairs, that will be looked at at any given time to calculate density. </help> - - <citations> - </citations> - + <expand macro="citations"/> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 23 10:25:36 2020 -0400 @@ -0,0 +1,16 @@ +<macros> + <token name="@VERSION@">1.8.2</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">snvphyl-tools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1099/mgen.0.000116</citation> + <yield/> + </citations> + </xml> +</macros>