comparison snpSift_annotate.xml @ 2:bf8c1526871b draft

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

1:98708b88af9f

<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.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" />
    <expand macro="version_command" />
    <command><![CDATA[
        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd 
        #if $annotate.id :
          -id
        #elif str($annotate.info_ids).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="" 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" />

2:bf8c1526871b

<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.1">
    <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" />
    <expand macro="version_command" />
    <command><![CDATA[
        @CONDA_SNPSIFT_JAR_PATH@ &&
        java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" $annotate_cmd
        #if $annotate.id :
          -id
        #elif str($annotate.info_ids).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="" 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" />