comparison annotate_variants.xml @ 1:99dfde12ee53 draft

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864

0:01e09a4cacf7

	  #end if
	  #if $snpeff_settings.filter:
	    #echo ' '.join(str($snpeff_settings.filter).split(','))
	  #end if
	  --ofile '$ofile'
	  --verbose
    ]]></command>

    <inputs>
        <param name="inputfile" type="data" format="vcf"
        label="VCF input file to be annotated" />

            <when value="select_by_name">
                <param name="annotation_source" type="text"
                label="Name of an installed SnpEff genome"
                help="Your input needs to exactly match the name of an installed SnpEff database.">
                    <validator type="expression" message="A SnpEff genome is required to run this tool.">value.strip()</validator>
                </param>
            </when>
        </conditional>
        <section name="codon_tables" title="Codon Table Configuration" expanded="false">
            <param name="genome_codon_table" type="text"
            label="Genome codon table"
            help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff." />
            <repeat name="table_specs" default="0" min="0"
            title="Codon tables to use for specific contigs"
            help="Use if certain contigs in the reference genome use a distinct codon table. A typical example is a mitochondrial genome contained as a contig in the reference genome. Contig/codon table assignments declared here will take precedence over a genome codon table set above.">
                <param name="contig" type="text" label="contig or chromosome name">
                    <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
                </param>
                <param name="table" type="text" label="uses codon table">
                    <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
                </param>
            </repeat>
        </section>
    	<section name="snpeff_settings" title="More SnpEff options" expanded="false">
            <param name="stats" type="boolean" checked="false"

1:99dfde12ee53

	  #end if
	  #if $snpeff_settings.filter:
	    #echo ' '.join(str($snpeff_settings.filter).split(','))
	  #end if
	  --ofile '$ofile'
	  --verbose --quiet
    ]]></command>

    <inputs>
        <param name="inputfile" type="data" format="vcf"
        label="VCF input file to be annotated" />

            <when value="select_by_name">
                <param name="annotation_source" type="text"
                label="Name of an installed SnpEff genome"
                help="Your input needs to exactly match the name of an installed SnpEff database.">
                    <validator type="expression" message="A SnpEff genome is required to run this tool.">value.strip()</validator>
                    <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in SnpEff genome names." />
                </param>
            </when>
        </conditional>
        <section name="codon_tables" title="Codon Table Configuration" expanded="false">
            <param name="genome_codon_table" type="text"
            label="Genome codon table"
            help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff.">
                <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
            </param>
            <repeat name="table_specs" default="0" min="0"
            title="Codon tables to use for specific contigs"
            help="Use if certain contigs in the reference genome use a distinct codon table. A typical example is a mitochondrial genome contained as a contig in the reference genome. Contig/codon table assignments declared here will take precedence over a genome codon table set above.">
                <param name="contig" type="text" label="contig or chromosome name">
                    <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
                    <expand macro="lex_sam_header" message="Non-ASCII characters are not allowed in contig/chromosome names" />
                </param>
                <param name="table" type="text" label="uses codon table">
                    <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
                    <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
                </param>
            </repeat>
        </section>
    	<section name="snpeff_settings" title="More SnpEff options" expanded="false">
            <param name="stats" type="boolean" checked="false"