comparison macros.xml @ 3:33fac436dd54 draft

planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 1056d5cc83082613f5d92b22b4e531fa9d505b91

2:eb5dcbebd242

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.1.3</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="main_parameters">
        <conditional name="main_params">
            <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
                <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>

                            <param name="gapextend" type="integer" min="0" value="1" label="BLAST gapextend" help="Cost to extend a gap"/>
                        </section>
                        <section name="blast_hits_usage" title="varVAMP settings for handling BLAST hits">
                            <param name="BLAST_MAX_DIFF" type="float" min="0" max="1" value="0.5" label="BLAST_MAX_DIFF" help="Minimal fraction of identity to primer to consider a BLAST hit an off-target primer binding site" />
                            <param name="BLAST_SIZE_MULTI" type="float" min="1" value="2" label="BLAST_SIZE_MULTI" help="Disregard off-target amplicons with a length greater than the configured maximal length of target amplicons multiplied by this value" />
                            <param name="BLAST_PENALTY" type="integer" min="0" value="50" label="BLAST_PENALTY" help="Extra penalty imposed on amplicons with off-target primer products; the default of 50 should be high enough to consider such amplicons only when no other amplicons without off-target products can be found." />
                        </section>
                    </when>
                </conditional>
            </when>
        </conditional>

3:33fac436dd54

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.2.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="main_parameters">
        <conditional name="main_params">
            <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
                <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>

                            <param name="gapextend" type="integer" min="0" value="1" label="BLAST gapextend" help="Cost to extend a gap"/>
                        </section>
                        <section name="blast_hits_usage" title="varVAMP settings for handling BLAST hits">
                            <param name="BLAST_MAX_DIFF" type="float" min="0" max="1" value="0.5" label="BLAST_MAX_DIFF" help="Minimal fraction of identity to primer to consider a BLAST hit an off-target primer binding site" />
                            <param name="BLAST_SIZE_MULTI" type="float" min="1" value="2" label="BLAST_SIZE_MULTI" help="Disregard off-target amplicons with a length greater than the configured maximal length of target amplicons multiplied by this value" />
                        </section>
                    </when>
                </conditional>
            </when>
        </conditional>