annotate remove.dists.xml @ 2:0df1987fb914 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

<tool profile="16.07" id="mothur_remove_dists" name="Remove.dists" version="@WRAPPER_VERSION@.0">
    <description>Removes distances from a phylip or column file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$accnos' accnos.dat &&
ln -s '$input.dist' input_dist.dat &&

echo 'remove.dists(
    accnos=accnos.dat,
    #if $input.source == "phylip":
        phylip=input_dist.dat
    #else
        column=input_dist.dat
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="source" type="select" label="Select input format">
                <option value="column">Pairwise Column Distance Matrix</option>
                <option value="phylip">Phylip Distance Matrix</option>
            </param>
            <when value="column">
                <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
            </when>
            <when value="phylip">
                <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
            </when>
        </conditional>
        <param argument="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="pick_dist" format_source="dist" from_work_dir="input_dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/>
    </outputs>
    <tests>
        <test>
            <param name="source" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
            <output name="pick_dist" ftype="mothur.square.dist">
                <assert_contents>
                    <expand macro="test-dist-format"/>
                    <has_text text="U68589"/>
                    <has_line_matching expression="^90$"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file.

.. _remove.dists: https://www.mothur.org/wiki/Remove.dists

    ]]></help>
    <expand macro="citations"/>
</tool>