comparison filter_vcf.xml @ 6:74f595df6e51 draft

Uploaded

5:e2ee6acf8752

  </stdio>
  <command interpreter="bash">
    filter_vcf.sh
	$output
	$input
    #if str($onlygood) == "false":
		onlygood
	#else
		NOTTHERE
	#end if

	#end for
  </command>

  <inputs>
    <param name="input" type="data" format="vcf" label="VCF File to filter" />

    <repeat name="snp_filter" title="SNP Filter" help="">
        <conditional name="snp_filter_type">
			<param name="snp_filter_type_selector" type="select" label="SNP Filter Type">
				<option value="gq_score_option">GQ score</option>

\-\-filters FILTERS, -f FILTERS	Filter(s) to apply as key:threshold pairs, separated by comma.

\-\-output OUTPUT, -o OUTPUT	Location for filtered VCF to be written.

  </help>
</tool>

6:74f595df6e51

  </stdio>
  <command interpreter="bash">
    filter_vcf.sh
	$output
	$input
    $ref_fa
    #if str($onlygood) == "false":
		onlygood
	#else
		NOTTHERE
	#end if

	#end for
  </command>

  <inputs>
    <param name="input" type="data" format="vcf" label="VCF File to filter" />

    <param name="ref_fa" type="data" format="fasta" label="Reference genome fasta file" help="REQUIRED."/>

    <repeat name="snp_filter" title="SNP Filter" help="">
        <conditional name="snp_filter_type">
			<param name="snp_filter_type_selector" type="select" label="SNP Filter Type">
				<option value="gq_score_option">GQ score</option>

\-\-filters FILTERS, -f FILTERS	Filter(s) to apply as key:threshold pairs, separated by comma.

\-\-output OUTPUT, -o OUTPUT	Location for filtered VCF to be written.

\-\-reference REFERENCE, -r REFERENCE   mpileup versions 1.3 and before do not output all positions. This is required to fix reference base in VCF.

\-\-only-good           Write only variants that PASS all filters (default all variants are written).

  </help>
</tool>