annotate dist.seqs.xml @ 10:4d76fba83f24 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab

<tool profile="16.07" id="mothur_dist_seqs" name="Dist.seqs" version="@WRAPPER_VERSION@.0">
    <description>calculate uncorrected pairwise distances between aligned sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&

echo 'dist.seqs(
    fasta=fasta.dat,
    #if $calc:
        calc=$calc,
    #end if
    countends=$countends,
    #if $cutoff:
        cutoff=$cutoff,
    #end if
    #if $output:
        output=$output,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Alignment Fasta"/>
        <param name="calc" type="select" label="calc - Calc Method - Gap Penality">
            <option value="" selected="true">use default</option>
            <option value="onegap">onegap - counts a string of gaps as a single gap</option>
            <option value="nogaps">nogaps - ignores gaps</option>
            <option value="eachgap ">eachgap - penalize each gap</option>
        </param>
        <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/>
        <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
            help="Do not save any distances larger than this, a common value would be 0.10"/>
        <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
            <option value="" selected="true">Default Column-Formatted Matrix</option>
            <option value="lt">Phylip formatted Lower Triangle Matrix</option>
            <option value="square">Phylip formatted Square Matrix</option>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
            <change_format>
                <when input="output" value="lt" format="mothur.lower.dist"/>
                <when input="output" value="square" format="mothur.square.dist"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test><!-- test with default params -->
            <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
            <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with all params custom -->
            <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
            <param name="calc" value="nogaps"/>
            <param name="countends" value="false"/>
            <param name="cutoff" value="0.3"/>
            <param name="output" value="lt"/>
            <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences.  The command will generate a column-formatted_distance_matrix_ that is compatible with the column option in the read.dist command. The command is also able to generate a phylip-formatted_distance_matrix_. There are several options for how to handle gap comparisons and terminal gaps.

.. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs

v.1.20.0: Updated to Mothur 1.33

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1371/journal.pcbi.1000844</citation>
    </expand>
</tool>