comparison snpEff.xml @ 5:2950d5afa3fe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

4:698ef30638a8

            mkdir $statsFile.files_path;
            mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#;
        #end if
        #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
          ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
          sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
        #end if
]]>
    </command>
    <inputs>
        <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>

        <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
            <option value="default" selected="true">Use default (based on input type)</option>
            <option value="-0">Force zero-based positions (both input and output)</option>
            <option value="-1">Force one-based positions (both input and output)</option>
        </param>
        <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
            <help>
               By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
               You can prepend any string you want to the chromosome name.
            </help>
            <validator type="regex" message="No whitespace allowed">^\S*$</validator>

5:2950d5afa3fe

            mkdir $statsFile.files_path;
            mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#;
        #end if
        #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
          ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
          sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
        #end if
]]>
    </command>
    <inputs>
        <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>

        <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
            <option value="default" selected="true">Use default (based on input type)</option>
            <option value="-0">Force zero-based positions (both input and output)</option>
            <option value="-1">Force one-based positions (both input and output)</option>
        </param>
        <param name="chr" type="text" label="Text to prepend to chromosome name">
            <help>
               By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
               You can prepend any string you want to the chromosome name.
            </help>
            <validator type="regex" message="No whitespace allowed">^\S*$</validator>