Mercurial > repos > ftouzain > vcfutils_vcf2fq
changeset 0:921286a54e95 draft default tip
Uploaded wrapper for vcutils.pl vcf2fq
| author | ftouzain |
|---|---|
| date | Thu, 22 Jun 2023 15:41:59 +0000 |
| parents | |
| children | |
| files | vcfutils_vcf2fq.xml |
| diffstat | 1 files changed, 52 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfutils_vcf2fq.xml Thu Jun 22 15:41:59 2023 +0000 @@ -0,0 +1,52 @@ +<tool id="vcfutils_vcf2fq" name="vcfutils_vcf2fq: convert vcf file to fastq file" version="1.16" python_template_version="3.9"> + <requirements> + <requirement type="package" version="1.16">bcftools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + vcfutils.pl vcf2fq -d '$min_depth' -D '$max_depth' -Q '$min_RMS_mapQ' -l '$filtering_window' '$all_sites_vcf_f' > '$fastq_f' + ]]></command> + <inputs> + <param type="data" name="all_sites_vcf_f" format="vcf" /> + <param type="integer" name="min_depth" label="min covereage depth" value="3" /> + <param type="integer" name="max_depth" label="max coverage depth" value="100000" /> + <param type="integer" name="min_RMS_mapQ" label="min RMS mapQ" value="10" /> + <param type="integer" name="filtering_window" label="filtering window" value="5" /> + </inputs> + <outputs> + <data name="fastq_f" format="fastq" /> + </outputs> + <tests> + <test> + <param name="all_sites_vcf_f" value="test_vcfutils_vcf2fq/all_sites.vcf"/> + <output name="fastq_f" file="test_vcfutils_vcf2fq/consensus.fastq"/> + </test> + </tests> + <help><![CDATA[ +[vcfutils_vcf2fq] +Aim: Deduce from vcf file output fastq file +in: +- vcf file with all sites +out: +- consensus fastq file + +usage: vcfutils.pl vcf2fq all_sites.vcf > consensus.fastq + +optional arguments: + -d INT minimum depth [3] + -D INT maximum depth [100000] + -Q INT min RMS mapQ [10] + -l INT INDEL filtering window [5] + ]]></help> + <citations> + <citation type="bibtex"> +@misc{vcfutils_vcf2fq, + author = {Li, Heng}, + year = {2009}, + title = {The Sequence Alignment/Map format and SAMtools}, + publisher = {}, + journal = {Bioinformatics}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002}, + }</citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + </citations> +</tool>