comparison snpSift_extractFields.xml @ 6:824f78c0d0df

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty

4:baf6602903e1

        > $output
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param name="extract" type="text" label="Extract" size="160" help="Need help? See below a few examples." />
        <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" />
        <param name="separator" type="text" value="" optional="true" label="multiple field separator" size="1" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values">
        </param>
        <param name="empty_text" type="text" value="" optional="true" label="empty field text" size="10" help="Represent empty fields with this value, rather than leaving them blank" >
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>

        MQ
        etc. (any info field available) 
    SnpEff 'ANN' fields:
        "ANN[*].ALLELE" (alias GENOTYPE)
        "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.)
        "ANN[*].IMPACT:" { HIGH, MODERATE, LOW, MODIFIER }
        "ANN[*].GENE:" Gene name (e.g. 'PSD3')
        "ANN[*].GENEID:" Gene ID
        "ANN[*].FEATURE
        " ANN[*].FEATUREID (alias TRID: Transcript ID)
        "ANN[*].BIOTYPE:" Biotype, as described by the annotations (e.g. 'protein_coding')
        "ANN[*].RANK:" Exon or Intron rank (i.e. exon number in a transcript)
        "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation
        "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation
        "ANN[*].CDNA_POS" (alias POS_CDNA)
        "ANN[*].CDNA_LEN" (alias LEN_CDNA)
        "ANN[*].CDS_POS" (alias POS_CDS)

6:824f78c0d0df

        > $output
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param name="extract" type="text" label="Extract" help="Need help? See below a few examples." />
        <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" />
        <param name="separator" type="text" value="" optional="true" label="multiple field separator" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values">
        </param>
        <param name="empty_text" type="text" value="" optional="true" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" >
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>

        MQ
        etc. (any info field available) 
    SnpEff 'ANN' fields:
        "ANN[*].ALLELE" (alias GENOTYPE)
        "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.)
        "ANN[*].IMPACT" { HIGH, MODERATE, LOW, MODIFIER }
        "ANN[*].GENE" Gene name (e.g. 'PSD3')
        "ANN[*].GENEID" Gene ID
        "ANN[*].FEATURE"
        "ANN[*].FEATUREID" (alias TRID: Transcript ID)
        "ANN[*].BIOTYPE" Biotype, as described by the annotations (e.g. 'protein_coding')
        "ANN[*].RANK" Exon or Intron rank (i.e. exon number in a transcript)
        "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation
        "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation
        "ANN[*].CDNA_POS" (alias POS_CDNA)
        "ANN[*].CDNA_LEN" (alias LEN_CDNA)
        "ANN[*].CDS_POS" (alias POS_CDS)