annotate trimal.xml @ 0:ebe28cac8d8b draft

planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671

<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>