comparison summary.shared.xml @ 3:2b8970aa8c5c draft

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

2:978f77d2117b

    </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.shared(
            shared=otu.dat,
            #if $groups:
                label=${ str($label).replace(",","-") },
            #end if
            #if $label:
                groups=${ str($groups).replace(",","-") },
            #end if
            #if $calc:
                calc=${ str($calc).replace(",","-") },
            #end if
            all=$all,
            distance=$distance,
            #if $subsample.use == "yes":
                #if $subsample.subsample:
                    subsample=$subsample.subsample,
                #else
                    subsample=T,
                #end if
                #if $subsample.iters:
                    iters=$subsample.iters,
                #end if
            #end if
            output=$output,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>

            <param name="otu" value="amazon.an.shared"/>
            <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsample -->
            <param name="otu" value="amazon.an.shared"/>
            <param name="use" value="yes"/>
            <param name="subsample" value="10"/>
            <param name="iters" value="42"/>
            <output name="summary" ftype="tabular">
                <assert_contents>

                </element>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file 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

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

3:2b8970aa8c5c

    </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.shared(
    shared=otu.dat,
    #if $groups:
        label=${ str($label).replace(",","-") },
    #end if
    #if $label:
        groups=${ str($groups).replace(",","-") },
    #end if
    #if $calc:
        calc=${ str($calc).replace(",","-") },
    #end if
    all=$all,
    distance=$distance,
    #if $subsample.use == "yes":
        #if $subsample.subsample:
            subsample=$subsample.subsample,
        #else
            subsample=T,
        #end if
        #if $subsample.iters:
            iters=$subsample.iters,
        #end if
    #end if
    output=$output,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>

            <param name="otu" value="amazon.an.shared"/>
            <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsample -->
            <param name="otu" value="amazon.mothur.shared"/>
            <param name="use" value="yes"/>
            <param name="subsample" value="10"/>
            <param name="iters" value="42"/>
            <output name="summary" ftype="tabular">
                <assert_contents>

                </element>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file 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

.. _shared: https://www.mothur.org/wiki/Shared_file
.. _group: https://www.mothur.org/wiki/Group_file
.. _summary.shared: https://www.mothur.org/wiki/Summary.shared

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