comparison normalize.shared.xml @ 2:0493525c9b4f draft

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

1:7f003a097b79

    </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 'normalize.shared(
            #if $otu.is_of_type("mothur.relabund"):
                relabund=otu.dat
            #elif $otu.is_of_type("mothur.shared"):
                shared=otu.dat,
                makerelabund=$makerelabund
            #end if
            #if $label:
                ,label=${ str($label).replace(",","-") }
            #end if
            #if $groups:
                ,groups=${ str($groups).replace(",","-") }
            #end if
            #if $method:
                ,method=${ str($method).replace(",","-") }
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
        <param name="label" type="select" multiple="true" label="label - OTU Labels">
            <expand macro="labeloptions"/>

        <param name="method" type="select" label="method - Normalization method">
            <option value="totalgroup" selected="true">Total Group</option>
            <option value="zscore">Z Score</option>
        </param>
        <param name="makerelabund" type="boolean" truevalue="true" falsevalue="false" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: norm.shared files collection">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>

        <test><!-- test default settings -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output_collection name="sharedfiles" count="36">
                <element name="0.26.norm" md5="73ad51ce74e5b3efbc1d9ec8ed6e1c07" ftype="mothur.shared"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test default settings -->
            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
            <param name="label" value="0.03,0.05,0.22,0.26"/>
            <param name="groups" value="forest,pasture"/>
            <param name="method" value="zscore"/>
            <output_collection name="sharedfiles" count="4">
                <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The normalize.shared_ command normalizes the number of sequences per group to a specified level.  The input is a shared_ or relabund_ file.

.. _shared: https://www.mothur.org/wiki/Shared_file
.. _relabund: https://www.mothur.org/wiki/Get.relabund
.. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared
]]>
    </help>
    <expand macro="citations"/>
</tool>

2:0493525c9b4f

    </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 'normalize.shared(
    #if $otu.is_of_type("mothur.relabund"):
        relabund=otu.dat
    #elif $otu.is_of_type("mothur.shared"):
        shared=otu.dat,
        makerelabund=$makerelabund
    #end if
    #if $label:
        ,label=${ str($label).replace(",","-") }
    #end if
    #if $groups:
        ,groups=${ str($groups).replace(",","-") }
    #end if
    #if $method:
        ,method=${ str($method).replace(",","-") }
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
        <param name="label" type="select" multiple="true" label="label - OTU Labels">
            <expand macro="labeloptions"/>

        <param name="method" type="select" label="method - Normalization method">
            <option value="totalgroup" selected="true">Total Group</option>
            <option value="zscore">Z Score</option>
        </param>
        <param name="makerelabund" type="boolean" truevalue="true" falsevalue="false" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: norm.shared files collection">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>

        <test><!-- test default settings -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output_collection name="sharedfiles" count="36">
                <element name="0.26.norm" md5="73ad51ce74e5b3efbc1d9ec8ed6e1c07" ftype="mothur.shared"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test default settings -->
            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
            <param name="label" value="0.03,0.05,0.22,0.26"/>
            <param name="groups" value="forest,pasture"/>
            <param name="method" value="zscore"/>
            <output_collection name="sharedfiles" count="4">
                <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The normalize.shared_ command normalizes the number of sequences per group to a specified level.  The input is a shared_ or relabund_ file.

.. _shared: https://www.mothur.org/wiki/Shared_file
.. _relabund: https://www.mothur.org/wiki/Get.relabund
.. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared

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