annotate get.otulist.xml @ 0:2e6fb8f23d5e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

<tool profile="16.07" id="mothur_get_otulist" name="Get.otulist" version="@WRAPPER_VERSION@.0">
    <description>Get otus for each distance in a otu list</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 "$otu" otu.dat &&

        echo 'get.otulist(
            list=otu.dat,
            #if $label:
                label=${ str($label).replace(",","-") },
            #end if
            sort=$sort
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected.">
            <expand macro="labeloptions"/>
        </param>
        <param name="sort" type="select" label="sort - select the output format" help="If otu is selected the output will be otu number followed by the list of names in that otu. If name is selected the output will be a sequence name followed by its otu number">
            <option value="otu" selected="true">otu</option>
            <option value="name">name</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="otufiles" type="list" label="${tool.name} on ${on_string}: OTUs per label">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu" format="mothur.list"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <output_collection name="otufiles" count="36">
                <element name="0.22" md5="9dfa8c449a45d66e7ae6b30b34a821cb" ftype="mothur.list"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="label" value="0.03,0.38,0.41,0.45"/>
            <output_collection name="otufiles" count="4">
                <element name="0.41" md5="b40486b3739a6d5b86459dc17a23c253" ftype="mothur.list"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU.

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

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