comparison trimal.xml @ 3:4769baf47b8d draft default tip

planemo upload for repository https://github.com/inab/trimal commit 3b2eb8e972bed82a1cd7c1e327b81ecfd994fb3d

2:0d53577b962f

                <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option>
                <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option>
                <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option>
                <option value="-strict">strict. (see User Guide)</option>
                <option value="-strictplus">strictplus. (see User Guide)</option>
                <option value="custom">Custom mode</option>
            </param>
            <when value="custom">
                <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gap threshold" help="1 - (fraction of sequences with a gap allowed). Range: [0 - 1]" multiple="false"/>
                <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="similarity threshold" help="Minimum average similarity allowed. Range: [0 - 1]" multiple="false"/>

    -nogaps                  Remove all positions with gaps in the alignment.
    -noallgaps               Remove columns composed only by gaps.
    -gappyout                Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
    -strict                  Use automatic selection on "strict" mode. (see User Guide).
    -strictplus              Use automatic selection on "strictplus" mode. (see User Guide).
    trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón.

Custom mode parameters
    -gt -gapthreshold <n>    1 - (fraction of sequences with a gap allowed).
    -st -simthreshold <n>    Minimum average similarity allowed.

3:4769baf47b8d

                <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option>
                <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option>
                <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option>
                <option value="-strict">strict. (see User Guide)</option>
                <option value="-strictplus">strictplus. (see User Guide)</option>
                <option value="-automated1">automated</option>
                <option value="custom">Custom mode</option>
            </param>
            <when value="custom">
                <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gap threshold" help="1 - (fraction of sequences with a gap allowed). Range: [0 - 1]" multiple="false"/>
                <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="similarity threshold" help="Minimum average similarity allowed. Range: [0 - 1]" multiple="false"/>

    -nogaps                  Remove all positions with gaps in the alignment.
    -noallgaps               Remove columns composed only by gaps.
    -gappyout                Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
    -strict                  Use automatic selection on "strict" mode. (see User Guide).
    -strictplus              Use automatic selection on "strictplus" mode. (see User Guide).
    -automated1              Use an heuristic method to decide which is the best automated method for a given MSA.
    trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón.

Custom mode parameters
    -gt -gapthreshold <n>    1 - (fraction of sequences with a gap allowed).
    -st -simthreshold <n>    Minimum average similarity allowed.