Mercurial > repos > iuc > trimal
diff trimal.xml @ 0:ebe28cac8d8b draft
planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
| author | iuc |
|---|---|
| date | Fri, 15 Nov 2024 08:59:26 +0000 |
| parents | |
| children | 2a156ec81e7a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimal.xml Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,131 @@ +<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> + <description>for automated alignment trimming</description> + <macros> + <token name="@TOOL_VERSION@">1.5</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <xrefs> + <xref type="bio.tools">trimal</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">trimal</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + trimal -in '$in' -out '$trimmed_output' -htmlout '$html_summary' ${out_format_selector} + #if $trimming_mode.mode_selector == "custom" + -gapthreshold $trimming_mode.gapthreshold + -simthreshold $trimming_mode.simthreshold + -cons $trimming_mode.cons + #else: + $trimming_mode.mode_selector + #end if + + ]]></command> + <inputs> + <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" /> + <conditional name="trimming_mode"> + <param name="mode_selector" type="select" label="Select trimming mode from the list"> + <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.</option> + <option value="-strict">strict - combine gappyout trimming with subsequent trimming based on an automatically selected similarity threshold. </option> + <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option> + <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option> + <option value="custom">custom mode - eliminates a specified set of columns defined by the user.</option> + </param> + <when value="-nogaps" /> + <when value="-noallgaps"/> + <when value="-gappyout"/> + <when value="-strict"/> + <when value="-strictplus"/> + <when value="-automated1"/> + <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)."/> + <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/> + <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="Minimum conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve."/> + </when> + </conditional> + <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list"> + <option value="-clustal">CLUSTAL format</option> + <option value="-fasta">FASTA format</option> + <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option> + <option value="-nbrf">NBRF/PIR format</option> + <option value="-nexus">NEXUS format</option> + <option value="-mega">MEGA format</option> + <option value="-phylip">PHYLIP/PHYLIP4 format</option> + <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option> + <option value="-phylip_paml">PHYLIP format compatible with PAML</option> + <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option> + <option value="-phylip3.2">PHYLIP3.2 format</option> + <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option> + </param> + </inputs> + <outputs> + <data name="trimmed_output" format="fasta" label="Trimmed alignment."> + <change_format> + <when input="out_format_selector" value="-fasta" format="fasta" /> + <when input="out_format_selector" value="-fasta_m10" format="fasta" /> + <when input="out_format_selector" value="-phylip" format="phylip" /> + <when input="out_format_selector" value="-phylip_m10" format="phylip" /> + <when input="out_format_selector" value="-phylip_paml" format="phylip" /> + <when input="out_format_selector" value="-phylip_paml_m10" format="phylip" /> + <when input="out_format_selector" value="-phylip3.2" format="phylip" /> + <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" /> + <when input="out_format_selector" value="-clustal" format="clustal" /> + <when input="out_format_selector" value="-mega" format="mega" /> + <when input="out_format_selector" value="-nbrf" format="pir" /> + <when input="out_format_selector" value="-nexus" format="nexus" /> + </change_format> + </data> + <data name="html_summary" format="html" label="trimal html summary."/> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="in" value="example.009.AA.fasta"/> + <param name="mode_selector" value="-gappyout" /> + <param name="out_format_selector" value="-mega" /> + <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/> + <output name="html_summary" file="trimmed_example.009.AA.html"/> + </test> + <test expect_num_outputs="2"> + <param name="in" value="example.009.AA.fasta"/> + <param name="mode_selector" value="custom" /> + <param name="gapthreshold" value="0.5" /> + <param name="simthreshold" value="0.5" /> + <param name="cons" value="5" /> + <param name="out_format_selector" value="-phylip_paml_m10" /> + <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/> + <output name="html_summary" file="custom_trimmed_example.009.AA.html"/> + </test> + </tests> + <help><![CDATA[ + +TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. + +TrimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. +These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, +the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment. + +TrimAl implements a series of automated algorithms that trim the alignment searching for optimum thresholds based on inherent characteristics +of the input alignment, to be used so that the signal-to-noise ratio after alignment trimming phase is increased. Learn more about the available trimming modes here: https://trimal.readthedocs.io/en/latest/algorithms.html + +Among trimAl's additional features, trimAl allows: + +- getting the complementary alignment (columns that were trimmed), +- to compute statistics from the alignment, +- to select the output file format, +- to get a summary of trimAl's trimming in HTML and SVG formats, +- and many other options. + +TrimAl webpage: https://trimal.readthedocs.io + +License +------- +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, the last available version. + ]]></help> + <citations> + <citation type="doi">doi:10.1093/bioinformatics/btp348</citation> + </citations> +</tool> \ No newline at end of file