comparison summary.shared.xml @ 2:88aa9d575274 draft

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

1:8e74259d96c3

    </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"/>

        </conditional>
        <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
            <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
            <option value="square">Phylip formatted Square Matrix</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: shared.summary"/>
        <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist">

    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <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>
                    <has_text text="forest"/>
                    <has_text text="pasture"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label and groups select and all calculators -->
            <param name="otu" value="amazon.an.shared"/>
            <param name="label" value="0.05,0.22,0.32"/>
            <param name="groups" value="forest,pasture"/>
            <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
            <output name="summary" md5="acd56d4ab09ec1c2117f5e4840a875a1" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with distance output collection -->
            <param name="otu" value="amazon.an.shared"/>
            <param name="distance" value="true"/>

                        <has_text text="forest"/>
                        <has_text text="pasture"/>
                    </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>

2:88aa9d575274

    </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"/>

        </conditional>
        <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
            <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
            <option value="square">Phylip formatted Square Matrix</option>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: shared.summary"/>
        <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist">

    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="otu" value="amazon.an.shared"/>
            <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <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>
                    <has_text text="forest"/>
                    <has_text text="pasture"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label and groups select and all calculators -->
            <param name="otu" value="amazon.an.shared"/>
            <param name="label" value="0.05,0.22,0.32"/>
            <param name="groups" value="forest,pasture"/>
            <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
            <output name="summary" md5="acd56d4ab09ec1c2117f5e4840a875a1" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with distance output collection -->
            <param name="otu" value="amazon.an.shared"/>
            <param name="distance" value="true"/>

                        <has_text text="forest"/>
                        <has_text text="pasture"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <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>