comparison snpSift_annotate.xml @ 11:b884686a80dc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a

10:93577c5e76ec

<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0">
    <description>SNPs from dbSnp</description>
    <!-- 
        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
    -->
    <expand macro="requirements" />
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <command>
        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
        #if $annotate.id :
          -id
        #elif $annotate.info_ids.__str__.strip() != '' :
          -info "$annotate.info_ids"
        #end if          
        -q $dbSnp $input > $output 
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
            help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
        <conditional name="annotate">
            <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
            <when value="id"/>
            <when value="info">
                <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs"
                    help="list is a comma separated list of fields. When blank, all INFO fields are included">    
                    <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
                </param>
            </when>
        </conditional>
        <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> 
            <help>
                This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
                Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). 
            </help>
            </param>
    </inputs>
    <expand macro="stdio" />
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
    <tests>
        <test>

11:b884686a80dc

<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0">
    <description>SNPs from dbSnp</description>
    <!--
        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
    -->
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd
        #if $annotate.id :
          -id
        #elif $annotate.info_ids.__str__.strip() != '' :
          -info "$annotate.info_ids"
        #end if
        -q $dbSnp $input > $output
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
            help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
        <conditional name="annotate">
            <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
            <when value="id"/>
            <when value="info">
                <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs"
                    help="list is a comma separated list of fields. When blank, all INFO fields are included">
                    <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
                </param>
            </when>
        </conditional>
        <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files">
            <help>
                This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
                Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
            </help>
            </param>
    </inputs>
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
    <tests>
        <test>