Mercurial > repos > nml > consolidate_vcfs
changeset 1:4c249c0aebad draft default tip
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
| author | nml |
|---|---|
| date | Tue, 23 Jun 2020 10:25:20 -0400 |
| parents | b42c82186e85 |
| children | |
| files | consolidate_vcfs.xml macros.xml test-data/expected_regions.txt test-data/expected_regions_disabled.txt test-data/expected_regions_empty.txt test-data/expected_regions_v3.txt test-data/freebayes/v3.bcf test-data/mpileup/v3.bcf test-data/v3.bcf.gz |
| diffstat | 9 files changed, 102 insertions(+), 38 deletions(-) [+] |
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--- a/consolidate_vcfs.xml Tue Aug 27 12:30:25 2019 -0400 +++ b/consolidate_vcfs.xml Tue Jun 23 10:25:20 2020 -0400 @@ -1,8 +1,9 @@ -<tool id="consolidate_vcfs" name="Consolidate VCFs" version ="1.8.2"> +<tool id="consolidate_vcfs" name="Consolidate VCFs" version ="@VERSION@+galaxy1"> <description>combine freebayes and mpileup files for use by vcf2snvalignment</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"><![CDATA[ #set $name = str($freebayes).split('/')[-1] @@ -24,6 +25,11 @@ bcftools index $name && #end if + ## If there is no density filtering performed we still need to output an empty file + #if not $use_density_filter: + echo '#No density filtering' > '$filtered_density' && + #end if + consolidate_vcfs.pl @@ -37,44 +43,37 @@ #set $path = str($mpileup).split('/')[-1] --mpileup "$path" - #set $path = str($path).split('/')[-1] - #if $filtered_density: - --filtered-density-out "$filtered_density" - #end if - - #if $use_density_filter.select_list == "no": + #if not $use_density_filter: --skip-density-filter #else - #if $use_density_filter.window_size: - --window-size "$use_density_filter.window_size" + #if $filtered_density: + --filtered-density-out '$filtered_density' #end if - #if $use_density_filter.threshold: - --density-threshold "$use_density_filter.threshold" + + #if $window_size: + --window-size "$window_size" + #end if + #if $threshold: + --density-threshold "$threshold" #end if #end if ##mark where the output files will be sent to, simply have to match them up later in the xml output section -o $bcf_combined + ]]> </command> <inputs> - <param name="coverage" type="integer" value="15" label="Minimum coverage"/> - <param name="mean_mapping" type="integer" value="30" label="Minimum mean mapping quality"/> - <param name="snv_abundance_ratio" type="text" value="0.75" optional="false" label="SNV abundance ratio"/> - <param name="freebayes" type="data" label="FreeBayes filtered BCF" help="" optional="false" format="bcf_bgzip,bcf" /> - <param name="mpileup" type="data" label="Mpileup BCF" help="" optional="false" format="bcf_bgzip,bcf" /> - <conditional name="use_density_filter"> - <param name="select_list" type="select" label= "SNV density filtering"> - <option value="yes">Apply</option> - <option value="no">Don't apply</option> - </param> - <when value="yes"> - <param name="window_size" type="integer" label="Size of search window" format="" optional="false" value="100"/> - <param name="threshold" type="integer" label="Density threshold cutoff" format="" optional="false" value="10"/> - </when> - <when value="no"> - </when> - </conditional> + <param name="coverage" type="integer" value="15" label="Minimum coverage" help="(--coverage-cutoff)" /> + <param name="mean_mapping" type="integer" value="30" label="Minimum mean mapping quality" help="(--min-mean-mapping)" /> + <param name="snv_abundance_ratio" type="text" value="0.75" optional="false" label="SNV abundance ratio" help="(--snv-abundance-ratio)" /> + <param name="freebayes" type="data" label="FreeBayes filtered BCF" optional="false" format="bcf_bgzip,bcf" help="(--vcfsplit)" /> + <param name="mpileup" type="data" label="Mpileup BCF" optional="false" format="bcf_bgzip,bcf" help="(--mpileup)" /> + <param name="use_density_filter" type="boolean" checked="true" label="Apply SNV density filtering" help="(--skip-density-filter)" /> + <param name="window_size" type="integer" min="1" label="SNV Density Filtering: Size of search window" format="" optional="false" value="500" + help="(--window-size) Size of the search window used to find high-density SNV regions. Only valid if density filtering is enabled." /> + <param name="threshold" type="integer" min="1" label="SNV Density Filtering: Density threshold cutoff" format="" optional="false" value="2" + help="(--density-threshold) The SNV threshold within a window to determine of this is a high-density SNV region. Only valid if density filtering is enabled." /> </inputs> <outputs> <data format="bcf_bgzip" name="bcf_combined"/> @@ -87,10 +86,11 @@ <param name="mpileup" value="mpileup/v1.bcf" /> <param name="mean_mapping" value="30" /> <param name="snv_abundance_ratio" value="0.75" /> + <param name="use_density_filter" value="true" /> <param name="window_size" value="500" /> <param name="threshold" value="2" /> <output name="bcf_combined" file="v1.bcf.gz" compare="sim_size" delta="500"/> - <output name="filtered_density" file="expected_regions.txt"/> + <output name="filtered_density" file="expected_regions_empty.txt"/> </test> <test> <param name="coverage" value="5"/> @@ -98,18 +98,63 @@ <param name="mpileup" value="mpileup/v2.bcf" /> <param name="mean_mapping" value="30" /> <param name="snv_abundance_ratio" value="0.75" /> + <param name="use_density_filter" value="true" /> <param name="window_size" value="500" /> <param name="threshold" value="2" /> <output name="bcf_combined" file="v2.bcf.gz" compare="sim_size" delta="500"/> - <output name="filtered_density" file="expected_regions.txt"/> + <output name="filtered_density" file="expected_regions_empty.txt"/> + </test> + <test> + <param name="coverage" value="5"/> + <param name="freebayes" value="freebayes/v3.bcf" /> + <param name="mpileup" value="mpileup/v3.bcf" /> + <param name="mean_mapping" value="30" /> + <param name="snv_abundance_ratio" value="0.75" /> + <param name="use_density_filter" value="true" /> + <param name="window_size" value="10" /> + <param name="threshold" value="3" /> + <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> + <output name="filtered_density" file="expected_regions_v3.txt"/> + </test> + <test> + <param name="coverage" value="5"/> + <param name="freebayes" value="freebayes/v3.bcf" /> + <param name="mpileup" value="mpileup/v3.bcf" /> + <param name="mean_mapping" value="30" /> + <param name="snv_abundance_ratio" value="0.75" /> + <param name="use_density_filter" value="true" /> + <param name="window_size" value="10" /> + <param name="threshold" value="4" /> + <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> + <output name="filtered_density" file="expected_regions_empty.txt"/> + </test> + <test> + <param name="coverage" value="5"/> + <param name="freebayes" value="freebayes/v3.bcf" /> + <param name="mpileup" value="mpileup/v3.bcf" /> + <param name="mean_mapping" value="30" /> + <param name="snv_abundance_ratio" value="0.75" /> + <param name="window_size" value="1" /> + <param name="threshold" value="2" /> + <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> + <output name="filtered_density" file="expected_regions_empty.txt"/> + </test> + <test> + <param name="coverage" value="5"/> + <param name="freebayes" value="freebayes/v3.bcf" /> + <param name="mpileup" value="mpileup/v3.bcf" /> + <param name="mean_mapping" value="30" /> + <param name="snv_abundance_ratio" value="0.75" /> + <param name="use_density_filter" value="false" /> + <param name="window_size" value="10" /> + <param name="threshold" value="3" /> + <output name="bcf_combined" file="v3.bcf.gz" compare="sim_size" delta="250"/> + <output name="filtered_density" file="expected_regions_disabled.txt"/> </test> </tests> <help> Merges variant and non-variant calls (in VCF format) produced from two independent base callers, FreeBayes, and SAMtools/BCFtools. Produces a merged set of high-quality variant and non-variant calls (in BCF format). Optionally, produces a list of SNV-dense regions above the passed thresholds. </help> - - <citations> - </citations> - + <expand macro="citations"/> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 23 10:25:20 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>
--- a/test-data/expected_regions.txt Tue Aug 27 12:30:25 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -#Calculation and writing of high density regions has completed.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_regions_disabled.txt Tue Jun 23 10:25:20 2020 -0400 @@ -0,0 +1,1 @@ +#No density filtering
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_regions_empty.txt Tue Jun 23 10:25:20 2020 -0400 @@ -0,0 +1,1 @@ +#Calculation and writing of high density regions has completed.