comparison snpSift_filter.xml @ 6:824f78c0d0df

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty

4:baf6602903e1

         > $output
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." />
        <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
        <conditional name="filtering">
            <param name="mode" type="select" label="Filter mode">
                <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
                <option value="field">Change the FILTER field, but retain all entries</option>

                <conditional name="replace">
                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" 
                           help="appends an ID tag to non-matching entry FILTER "/>
                    <when value="no"/>
                    <when value="yes">
                        <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10"
                               help="Default ID is 'SnpSift'"/>
                    </when>
                </conditional>
                <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
                <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/>
            </when>
        </conditional>
    </inputs>
    <configfiles>
        <configfile name="exprFile">

        </output>
        </test>

        <test>
        <param name="input" ftype="vcf" value="test01.vcf"/>
        <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/>
        <param name="mode" value="entries"/>
        <output name="output">
            <assert_contents>
            <has_text text="20175" />
            <has_text text="35549" />

6:824f78c0d0df

         > $output
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." />
        <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
        <conditional name="filtering">
            <param name="mode" type="select" label="Filter mode">
                <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
                <option value="field">Change the FILTER field, but retain all entries</option>

                <conditional name="replace">
                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" 
                           help="appends an ID tag to non-matching entry FILTER "/>
                    <when value="no"/>
                    <when value="yes">
                        <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." 
                               help="Default ID is 'SnpSift'"/>
                    </when>
                </conditional>
                <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." />
                <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." />
            </when>
        </conditional>
    </inputs>
    <configfiles>
        <configfile name="exprFile">

        </output>
        </test>

        <test>
        <param name="input" ftype="vcf" value="test01.vcf"/>
        <param name="expr" value="(POS >= 20175) &amp; (POS &lt; 35549)"/>
        <param name="mode" value="entries"/>
        <output name="output">
            <assert_contents>
            <has_text text="20175" />
            <has_text text="35549" />