comparison vcfvcfintersect.xml @ 4:6f6bf10618d7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582

3:1bc1b2b8b341

<tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@.0">
    <description>Intersect two VCF datasets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            </param>
            <when value="no" />
            <when value="use_adv_controls">
                <param name="adv_options_input" type="text" value="-t &quot;vcfvcf-intersect-result&quot;"
                    label="Enter additional command line options described in the help section below"
                    help="such as -m, -t, -V, -M, and -T" />
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                    </valid>
                    <mapping initial="none">
                        <add source="&apos;" target="__sq__"/>
                    </mapping>
                </sanitizer>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="vcf" name="out_file1" />

            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="vcflib-test-genome-phix.fa" />
            <param name="isect_union" value="-i" />
            <param name="invert" value="False" />
            <param name="loci" value="False" />
            <patam name="adv_options_selector" value="no" />
            <param name="window_size" value="30" />
            <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
            <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
            <param name="isect_union" value="-u" />
            <param name="invert" value="False" />
            <param name="loci" value="False" />
            <patam name="adv_options_selector" value="no" />
            <param name="window_size" value="30" />
            <param name="ref_file" value="vcflib-test-genome-phix.fa" />
            <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
        </test>
    </tests>

4:6f6bf10618d7

<tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@+galaxy0">
    <description>Intersect two VCF datasets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            </param>
            <when value="no" />
            <when value="use_adv_controls">
                <param name="adv_options_input" type="text" value="-t &quot;vcfvcf-intersect-result&quot;"
                    label="Enter additional command line options described in the help section below"
                    help="such as -m, -t, -V, -M, and -T">
                    <sanitizer>
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping initial="none">
                            <add source="&apos;" target="__sq__"/>
                        </mapping>
                    </sanitizer>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="vcf" name="out_file1" />

            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="vcflib-test-genome-phix.fa" />
            <param name="isect_union" value="-i" />
            <param name="invert" value="False" />
            <param name="loci" value="False" />
            <param name="adv_options_selector" value="no" />
            <param name="window_size" value="30" />
            <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
            <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
            <param name="isect_union" value="-u" />
            <param name="invert" value="False" />
            <param name="loci" value="False" />
            <param name="adv_options_selector" value="no" />
            <param name="window_size" value="30" />
            <param name="ref_file" value="vcflib-test-genome-phix.fa" />
            <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
        </test>
    </tests>