comparison snpEff.xml @ 26:5b80f544c67f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51

25:5c7b70713fb5

<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy1">
    <description> annotate variants</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirement" />
    </requirements>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        snpEff @JAVA_OPTIONS@ eff
        -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
        #if $spliceSiteSize and str($spliceSiteSize) != '':
          -spliceSiteSize "$spliceSiteSize"
        #end if

        #end if
        #if $transcripts
          -onlyTr '$transcripts'
        #end if
        #if $intervals     ### fix this for multiple dataset input
          -interval '$intervals'
        #end if
        #if $statsFile:
          -stats '$statsFile'
        #end if
        #if $csvStats:

                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).

26:5b80f544c67f

<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
    <description> annotate variants</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirement" />
    </requirements>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        #if $intervals 
            ln -s '${intervals}' intervals.bed &&
        #end if 
        snpEff @JAVA_OPTIONS@ eff
        -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
        #if $spliceSiteSize and str($spliceSiteSize) != '':
          -spliceSiteSize "$spliceSiteSize"
        #end if

        #end if
        #if $transcripts
          -onlyTr '$transcripts'
        #end if
        #if $intervals     ### fix this for multiple dataset input
          -interval intervals.bed
        #end if
        #if $statsFile:
          -stats '$statsFile'
        #end if
        #if $csvStats:

                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                </assert_contents>
            </output>
        </test>
        <!-- Test interval option-->
        <test>
            <param name="input" ftype="vcf" value="input.vcf"/>
            <param name="inputFormat" value="vcf"/>
            <param name="outputFormat" value="vcf"/>
            <param name="genomeSrc" value="named"/>
            <param name="interval" value="intervals.bed"/>
            <param name="genome_version" value="ebola_zaire"/>
            <param name="udLength" value="0"/>
            <param name="generate_stats" value="false"/>
            <output name="snpeff_output">
                <assert_contents>
                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).