comparison amplican.xml @ 1:8c1bba8d544a draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 902dc45a1d133b86b99f27d9902d642e475a3e87"

0:71adaaace336

            <param argument="gap_opening" type="integer" min="0" max="40" value="25" label="Gap opening" help="The opening gap score" />
            <param argument="gap_extension" type="integer" min="0" max="40" value="0" label="Gap extension" help="The gap extension score" />
            <param argument="primer_mismatch" type="integer" min="0" max="40" value="0" label="Primer mismatch" help="Decide how many mismatches are allowed during primer matching of the reads, that groups reads by experiments. When primer_mismatch = 0 no mismatches are allowed, which can increase number of unasssigned read" />
            <param argument="donor_mismatch" type="integer" min="0" max="40" value="3" label="Donor mismatch" help="How many events of length 1 (mismatches, deletions and insertions of length 1) are allowed when aligning toward the donor template. This parameter is only used when donor template is specified. The higher the parameter the less strict will be algorithm accepting read as HDR. Set to 0 if only perfect alignments to the donor template marked as HDR, unadvised due to error rate of the sequencers" />
            <section name="scoring_matrix" title="Scoring matrix options" expanded="False">
                <param argument="match_scoring" type="integer" min="0" max="20" value="5" label="Match scoring" help="TODO" />
                <param argument="mismatch_scoring" type="integer" min="-20" max="0" value="-4" label="Mismatch scoring" help="TODO" />
                <param argument="base_only" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Base only" help="TODO" />
                <param argument="scoring_type" type="select" label="Scoring matrix type" help="TODO">
                    <option value="DNA" selected="true">DNA</option>
                    <option value="RNA">RNA</option>
                </param>
            </section>
        </section>

1:8c1bba8d544a

            <param argument="gap_opening" type="integer" min="0" max="40" value="25" label="Gap opening" help="The opening gap score" />
            <param argument="gap_extension" type="integer" min="0" max="40" value="0" label="Gap extension" help="The gap extension score" />
            <param argument="primer_mismatch" type="integer" min="0" max="40" value="0" label="Primer mismatch" help="Decide how many mismatches are allowed during primer matching of the reads, that groups reads by experiments. When primer_mismatch = 0 no mismatches are allowed, which can increase number of unasssigned read" />
            <param argument="donor_mismatch" type="integer" min="0" max="40" value="3" label="Donor mismatch" help="How many events of length 1 (mismatches, deletions and insertions of length 1) are allowed when aligning toward the donor template. This parameter is only used when donor template is specified. The higher the parameter the less strict will be algorithm accepting read as HDR. Set to 0 if only perfect alignments to the donor template marked as HDR, unadvised due to error rate of the sequencers" />
            <section name="scoring_matrix" title="Scoring matrix options" expanded="False">
                <param argument="match_scoring" type="integer" min="0" max="20" value="5" label="Match scoring"/>
                <param argument="mismatch_scoring" type="integer" min="-20" max="0" value="-4" label="Mismatch scoring"/>
                <param argument="base_only" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Base only" />
                <param argument="scoring_type" type="select" label="Scoring matrix type">
                    <option value="DNA" selected="true">DNA</option>
                    <option value="RNA">RNA</option>
                </param>
            </section>
        </section>