comparison kggseq_variant_selection.xml @ 3:c758125c56d8 draft

Update to KggSeq release 0.8 (23/Apr./2015)

2:e1a21c2f4997

<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.2">
  <description></description>
  <requirements>
    <requirement type="package" version="0.7_20150118">kggseq</requirement>
  </requirements>
  <command>
java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
## Environmental settings
--buildver hg19

--ped-file $pedFile
--db-gene $db_gene
$composite_subject_id

## Variant and genotype filters
$pass_variant_only
#if str($variant_genotype_filters.variant_genotype_filters_select) == "yes"
  --seq-qual $variant_genotype_filters.seq_qual
  --seq-mq $variant_genotype_filters.seq_mq
  --seq-sb $variant_genotype_filters.seq_sb
  --seq-fs $variant_genotype_filters.seq_fs
  --min-heta $variant_genotype_filters.min_heta

      <option value="gencode">gencode: The GENCODE gene sets. Note: GENCODE contains similar number of coding genes but more transcripts than RefGene. It HAS the mitochondria gene definition</option>
      <option value="knowngene">knowngene: The UCSC knonwGene datasase compiled by UCSC from hg19 knownGene</option>
      <option value="ensembl">ensembl: The Ensembl gene datasase compiled by UCSC from hg19 ensGene</option>
      <validator type="no_options" message="Select at least one database" />
    </param>
    <param name="pass_variant_only" type="boolean" truevalue="--vcf-filter-in PASS" falsevalue="" checked="true" label="Don't include filtered loci (--vcf-filter-in PASS)" help="Keep only variants with FILTER equal to PASS" />

    <!-- Variant and genotype quality control -->
    <conditional name="variant_genotype_filters">
      <param name="variant_genotype_filters_select" type="select" label="Specify variant and genotype quality filters?">
        <option value="yes">Yes</option>
        <option value="no" selected="true">No</option>
      </param>
      <when value="yes">
        <param name="seq_qual" type="integer" value="50" label="Minimum overall Phred-scaled sequencing quality score for the variant (--seq-qual)" />
        <param name="seq_mq" type="integer" value="20" label="Minimum overall Phred-scaled mapping quality score for the variant (--seq-mq)" />
        <param name="seq_sb" type="float" value="-10" label="Maximal overall strand bias score for the variant (--seq-sb)" />
        <param name="seq_fs" type="integer" value="60" label="Maximal overall strand bias Phred-scaled p-value (using Fisher's exact test) for the variant (--seq-fs)" />
        <param name="min_heta" type="integer" value="0" label="Minimal observed number of heterozygote genotypes in cases (the affected) (--min-heta)" />

      </param>
      <when value="yes">
        <param name="gene_features" type="select" display="checkboxes" multiple="true" label="Select gene features (--gene-feature-in)" help="Variants falling outside the selected regions will be excluded">
          <option value="0" selected="true">Frame-shift</option>
          <option value="1" selected="true">Loss of amino acids</option>
          <option value="2" selected="true">Loss of stop codon (TAG, TAA, TGA)</option>
          <option value="3" selected="true">Gain of stop codon (TAG, TAA, TGA)</option>
          <option value="4" selected="true">Missense</option>
          <option value="5" selected="true">Splicing</option>
          <option value="6">Synonymous</option>
          <option value="7">Exonic</option>
          <option value="8">5-UTR</option>
          <option value="9">3-UTR</option>
          <option value="10">Intronic</option>
          <option value="11">Upstream of transcription start site</option>
          <option value="12">Downstream of transcription end site</option>
          <option value="13">ncRNA</option>
          <option value="14">Intergenic</option>
          <option value="15">Monomorphic</option>
          <option value="16">Unknown</option>
        </param>
        <param name="splicing" type="integer" value="2" label="Window size in base-pair around the splicing junction to flag the variant as splicing (--splicing)" />
        <param name="neargene" type="integer" value="1000" label="Size in base-pair of region upstream and downstream (--neargene)" />
      </when>
      <when value="no" />

3:c758125c56d8

<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.3">
  <description></description>
  <requirements>
    <requirement type="package" version="0.8_20150423 ">kggseq</requirement>
  </requirements>
  <command>
java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
## Environmental settings
--buildver hg19

--ped-file $pedFile
--db-gene $db_gene
$composite_subject_id

## Variant and genotype filters
#if str($variant_genotype_filters.variant_genotype_filters_select) == "yes"
  $variant_genotype_filters.pass_variant_only
  --seq-qual $variant_genotype_filters.seq_qual
  --seq-mq $variant_genotype_filters.seq_mq
  --seq-sb $variant_genotype_filters.seq_sb
  --seq-fs $variant_genotype_filters.seq_fs
  --min-heta $variant_genotype_filters.min_heta

      <option value="gencode">gencode: The GENCODE gene sets. Note: GENCODE contains similar number of coding genes but more transcripts than RefGene. It HAS the mitochondria gene definition</option>
      <option value="knowngene">knowngene: The UCSC knonwGene datasase compiled by UCSC from hg19 knownGene</option>
      <option value="ensembl">ensembl: The Ensembl gene datasase compiled by UCSC from hg19 ensGene</option>
      <validator type="no_options" message="Select at least one database" />
    </param>

    <!-- Variant and genotype quality control -->
    <conditional name="variant_genotype_filters">
      <param name="variant_genotype_filters_select" type="select" label="Specify variant and genotype quality filters?">
        <option value="yes">Yes</option>
        <option value="no" selected="true">No</option>
      </param>
      <when value="yes">
        <param name="pass_variant_only" type="boolean" truevalue="--vcf-filter-in PASS" falsevalue="" checked="true" label="Don't include filtered loci (--vcf-filter-in PASS)" help="Keep only variants with FILTER equal to PASS" />
        <param name="seq_qual" type="integer" value="50" label="Minimum overall Phred-scaled sequencing quality score for the variant (--seq-qual)" />
        <param name="seq_mq" type="integer" value="20" label="Minimum overall Phred-scaled mapping quality score for the variant (--seq-mq)" />
        <param name="seq_sb" type="float" value="-10" label="Maximal overall strand bias score for the variant (--seq-sb)" />
        <param name="seq_fs" type="integer" value="60" label="Maximal overall strand bias Phred-scaled p-value (using Fisher's exact test) for the variant (--seq-fs)" />
        <param name="min_heta" type="integer" value="0" label="Minimal observed number of heterozygote genotypes in cases (the affected) (--min-heta)" />

      </param>
      <when value="yes">
        <param name="gene_features" type="select" display="checkboxes" multiple="true" label="Select gene features (--gene-feature-in)" help="Variants falling outside the selected regions will be excluded">
          <option value="0" selected="true">Frame-shift</option>
          <option value="1" selected="true">Loss of amino acids</option>
          <option value="2" selected="true">Loss of start codon</option>
          <option value="3" selected="true">Loss of stop codon (TAG, TAA, TGA)</option>
          <option value="4" selected="true">Gain of stop codon (TAG, TAA, TGA)</option>
          <option value="5" selected="true">Splicing</option>
          <option value="6" selected="true">Missense</option>
          <option value="7">Synonymous</option>
          <option value="8">Exonic</option>
          <option value="9">5-UTR</option>
          <option value="10">3-UTR</option>
          <option value="11">Intronic</option>
          <option value="12">Upstream of transcription start site</option>
          <option value="13">Downstream of transcription end site</option>
          <option value="14">ncRNA</option>
          <option value="15">Intergenic</option>
          <option value="16">Monomorphic</option>
          <option value="17">Unknown</option>
        </param>
        <param name="splicing" type="integer" value="2" label="Window size in base-pair around the splicing junction to flag the variant as splicing (--splicing)" />
        <param name="neargene" type="integer" value="1000" label="Size in base-pair of region upstream and downstream (--neargene)" />
      </when>
      <when value="no" />