comparison vcffilter.xml @ 8:81972652519c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503

7:eae7c08ebb6f

<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2">
    <description>filter VCF data in a variety of attributes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        <repeat name="filter_repeat" title="more filters" min="1">
            <param name="filter_type" type="select" label="Select the filter type">
                <option value="-f">Info filter (-f)</option>
                <option value="-g">Genotype filter (-g)</option>
            </param>
            <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filterting value" help="See explanation of filtering options below">
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                        <remove value="&quot;"/>
                    </valid>
                    <mapping initial="none">
                        <add source="&apos;" target=""/>
                        <add source="&quot;" target=""/>
                    </mapping>
                </sanitizer>
            </param>
        </repeat>
        <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
        <param name="tag_pass" argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/>
        <param name="tag_fail" argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/>

        <test>
            <param name="filter_repeat_0|filter_type" value="-f"/>
            <param name="filter_repeat_0|filter_value" value="DP &gt; 10"/>
            <param name="input1" value="vcflib.vcf"/>
            <output name="out_file1" file="vcffilter-test1.vcf"/>
        </test>
    </tests>
    <help><![CDATA[
You can specify the following options within the **Specify filtering expression** box in any combination::

8:81972652519c

<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy3">
    <description>filter VCF data in a variety of attributes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        <repeat name="filter_repeat" title="more filters" min="1">
            <param name="filter_type" type="select" label="Select the filter type">
                <option value="-f">Info filter (-f)</option>
                <option value="-g">Genotype filter (-g)</option>
            </param>
            <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filtering value" help="See explanation of filtering options below">
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                        <remove value="&quot;"/>
                    </valid>
                    <mapping initial="none">
                        <add source="&apos;" target=""/>
                        <add source="&quot;" target=""/>
                    </mapping>
                </sanitizer>
                <validator type="expression" message="Invalid operator provided, valid operators are =, !, &lt;, &gt;, |, &amp;.">value is not None and not any(x in value for x in ["&lt;=", "=&lt;", "&gt;=", "=&gt;"])</validator>
            </param>
        </repeat>
        <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
        <param name="tag_pass" argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/>
        <param name="tag_fail" argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/>

        <test>
            <param name="filter_repeat_0|filter_type" value="-f"/>
            <param name="filter_repeat_0|filter_value" value="DP &gt; 10"/>
            <param name="input1" value="vcflib.vcf"/>
            <output name="out_file1" file="vcffilter-test1.vcf"/>
        </test>
        <test>
            <param name="filter_repeat_0|filter_type" value="-f"/>
            <param name="filter_repeat_0|filter_value" value="!( DP &gt; 10 )"/>
            <param name="invert" value="true"/>
            <param name="input1" value="vcflib.vcf"/>
            <output name="out_file1" file="vcffilter-test2.vcf"/>
        </test>
    </tests>
    <help><![CDATA[
You can specify the following options within the **Specify filtering expression** box in any combination::