comparison summary.single.xml @ 1:6c3b672ac325 draft

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

0:b32ea8b26bda

    <description>Summary of calculator values for OTUs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        ## create symlinks to input datasets
        ln -s "$otu" otu.dat &&

        echo 'summary.single(
            #if $otu.is_of_type("mothur.rabund"):

                #end if
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
            && mv otu.ave-std.summary otu.ave-std
        #end if
    ]]></command>
    <inputs>

    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documenation**

The summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group_ file.  This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _group: http://www.mothur.org/wiki/Group_file
.. _summary.single: http://www.mothur.org/wiki/Summary.single
]]>
    </help>
    <expand macro="citations"/>
</tool>

1:6c3b672ac325

    <description>Summary of calculator values for OTUs</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 'summary.single(
            #if $otu.is_of_type("mothur.rabund"):

                #end if
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
        #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
            && mv otu.ave-std.summary otu.ave-std
        #end if
    ]]></command>
    <inputs>

    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group_ file.  This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators

.. _group: https://www.mothur.org/wiki/Group_file
.. _summary.single: https://www.mothur.org/wiki/Summary.single
]]>
    </help>
    <expand macro="citations"/>
</tool>