view vcfutils_vcf2fq.xml @ 0:921286a54e95 draft default tip

Uploaded wrapper for vcutils.pl vcf2fq

<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>