comparison lastz_wrapper.xml @ 4:60afcc2c1d05 draft

planemo upload commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1

3:d054d95585b1

                </param>
                <param name="chain" type="select" label="Perform chaining of HSPs?">
                    <option value="nochain">No</option>
                    <option value="chain">Yes</option>
                </param>
                <param name="O" type="integer" size="5" value="400" label="Gap opening penalty"/>
                <param name="E" type="integer" size="5" value="30" label="Gap extension penalty"/>
                <param name="X" type="integer" size="5" value="910" label="X-drop threshold"/>
                <param name="Y" type="integer" size="5" value="9370" label="Y-drop threshold"/>
                <param name="K" type="integer" size="5" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/>
                <param name="L" type="integer" size="5" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/>
                <param name="entropy" type="select" label="Involve entropy when filtering HSPs?">
                    <option value="noentropy">No</option>
                    <option value="entropy">Yes</option>
                </param>
            </when>   

            <param name="how_to_name" type="select" label="Do you want to modify the reference name?">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="ref_name" type="text" size="25" value="Type sequence name here" label="Enter name for the Reference sequence"/>
            </when>
            <when value="no" />
        </conditional>
        <param name="min_ident" type="integer" size="3" value="0" label="Do not report matches below this identity (%)"/>
        <param name="max_ident" type="integer" size="3" value="100" label="Do not report matches above this identity (%)"/>
        <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this percentage of each read"/>
        <param name="unmask" type="select" label="Convert lowercase bases to uppercase">
            <option value="yes">Yes</option>
            <option value="no">No</option>
        </param>
    </inputs>

4:60afcc2c1d05

                </param>
                <param name="chain" type="select" label="Perform chaining of HSPs?">
                    <option value="nochain">No</option>
                    <option value="chain">Yes</option>
                </param>
                <param name="O" type="integer" value="400" label="Gap opening penalty"/>
                <param name="E" type="integer" value="30" label="Gap extension penalty"/>
                <param name="X" type="integer" value="910" label="X-drop threshold"/>
                <param name="Y" type="integer" value="9370" label="Y-drop threshold"/>
                <param name="K" type="integer" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/>
                <param name="L" type="integer" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/>
                <param name="entropy" type="select" label="Involve entropy when filtering HSPs?">
                    <option value="noentropy">No</option>
                    <option value="entropy">Yes</option>
                </param>
            </when>   

            <param name="how_to_name" type="select" label="Do you want to modify the reference name?">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="ref_name" type="text" value="Type sequence name here" label="Enter name for the Reference sequence"/>
            </when>
            <when value="no" />
        </conditional>
        <param name="min_ident" type="integer" value="0" label="Do not report matches below this identity (%)"/>
        <param name="max_ident" type="integer" value="100" label="Do not report matches above this identity (%)"/>
        <param name="min_cvrg" type="integer" value="0" label="Do not report matches that cover less than this percentage of each read"/>
        <param name="unmask" type="select" label="Convert lowercase bases to uppercase">
            <option value="yes">Yes</option>
            <option value="no">No</option>
        </param>
    </inputs>