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planemo upload for repository https://github.com/inab/trimal commit 3b2eb8e972bed82a1cd7c1e327b81ecfd994fb3d
author padge
date Thu, 19 Oct 2023 16:50:00 +0000
parents 0d53577b962f
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2:0d53577b962f 3:4769baf47b8d
21 <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option> 21 <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option>
22 <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option> 22 <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option>
23 <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option> 23 <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option>
24 <option value="-strict">strict. (see User Guide)</option> 24 <option value="-strict">strict. (see User Guide)</option>
25 <option value="-strictplus">strictplus. (see User Guide)</option> 25 <option value="-strictplus">strictplus. (see User Guide)</option>
26 <option value="-automated1">automated</option>
26 <option value="custom">Custom mode</option> 27 <option value="custom">Custom mode</option>
27 </param> 28 </param>
28 <when value="custom"> 29 <when value="custom">
29 <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"/> 30 <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"/>
30 <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"/> 31 <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"/>
90 -nogaps Remove all positions with gaps in the alignment. 91 -nogaps Remove all positions with gaps in the alignment.
91 -noallgaps Remove columns composed only by gaps. 92 -noallgaps Remove columns composed only by gaps.
92 -gappyout Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide). 93 -gappyout Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
93 -strict Use automatic selection on "strict" mode. (see User Guide). 94 -strict Use automatic selection on "strict" mode. (see User Guide).
94 -strictplus Use automatic selection on "strictplus" mode. (see User Guide). 95 -strictplus Use automatic selection on "strictplus" mode. (see User Guide).
96 -automated1 Use an heuristic method to decide which is the best automated method for a given MSA.
95 trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón. 97 trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón.
96 98
97 Custom mode parameters 99 Custom mode parameters
98 -gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed). 100 -gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed).
99 -st -simthreshold <n> Minimum average similarity allowed. 101 -st -simthreshold <n> Minimum average similarity allowed.