Mercurial > repos > nml > consolidate_vcfs
changeset 0:b42c82186e85 draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
| author | nml |
|---|---|
| date | Tue, 27 Aug 2019 12:30:25 -0400 |
| parents | |
| children | 4c249c0aebad |
| files | consolidate_vcfs.xml test-data/expected_regions.txt test-data/freebayes/v1.bcf test-data/freebayes/v2.bcf test-data/mpileup/v1.bcf test-data/mpileup/v2.bcf test-data/v1.bcf.gz test-data/v2.bcf.gz |
| diffstat | 8 files changed, 116 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consolidate_vcfs.xml Tue Aug 27 12:30:25 2019 -0400 @@ -0,0 +1,115 @@ +<tool id="consolidate_vcfs" name="Consolidate VCFs" version ="1.8.2"> + <description>combine freebayes and mpileup files for use by vcf2snvalignment</description> + <requirements> + <requirement type="package" version="1.8.2">snvphyl-tools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + #set $name = str($freebayes).split('/')[-1] + ln -f -s $freebayes && + + #if $freebayes.metadata.bcf_index: + ln -s '${$freebayes.metadata.bcf_index}' ${name}.csi && + #else + bcftools index $name && + #end if + + + #set $name = str($mpileup).split('/')[-1] + ln -f -s $mpileup && + + #if $mpileup.metadata.bcf_index: + ln -s '${$mpileup.metadata.bcf_index}' ${name}.csi && + #else + bcftools index $name && + #end if + + consolidate_vcfs.pl + + + -c "$coverage" + --min-mean-mapping "$mean_mapping" + --snv-abundance-ratio "$snv_abundance_ratio" + + #set $path = str($freebayes).split('/')[-1] + --vcfsplit "$path" + + #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": + --skip-density-filter + #else + #if $use_density_filter.window_size: + --window-size "$use_density_filter.window_size" + #end if + #if $use_density_filter.threshold: + --density-threshold "$use_density_filter.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> + </inputs> + <outputs> + <data format="bcf_bgzip" name="bcf_combined"/> + <data format="txt" name="filtered_density" label="High density regions"/> + </outputs> + <tests> + <test> + <param name="coverage" value="5"/> + <param name="freebayes" value="freebayes/v1.bcf" /> + <param name="mpileup" value="mpileup/v1.bcf" /> + <param name="mean_mapping" value="30" /> + <param name="snv_abundance_ratio" value="0.75" /> + <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"/> + </test> + <test> + <param name="coverage" value="5"/> + <param name="freebayes" value="freebayes/v2.bcf" /> + <param name="mpileup" value="mpileup/v2.bcf" /> + <param name="mean_mapping" value="30" /> + <param name="snv_abundance_ratio" value="0.75" /> + <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"/> + </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> + +</tool>