comparison get.dists.xml @ 3:56ca2af78a1c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4

2:0f076fb8f068

    </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 'get.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>

            <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
            <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.

.. _get.dists: https://www.mothur.org/wiki/Get.dists

v.1.20.0: Updated to Mothur 1.33
]]>
    </help>
    <expand macro="citations"/>
</tool>

3:56ca2af78a1c

    </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 'get.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>

            <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
            <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.

.. _get.dists: https://www.mothur.org/wiki/Get.dists

v.1.20.0: Updated to Mothur 1.33

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