comparison dist.shared.xml @ 5:7c8b0d0d792a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173

4:30b6caefc7a0

        </conditional>
        <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
            <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"/>
        <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"/>

        <test><!-- test with defaults -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output_collection name="distfiles" count="72">
                <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label,group select and all calculators -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.05,0.22"/>
            <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,structeuclidean,structpearson,sharednseqs,sharedobserved"/>
            <output_collection name="distfiles" count="74">
                <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsampling without specifying size -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.03,0.33"/>

                        <has_text text="forest"/>
                        <has_text text="pasture"/>
                    </assert_contents>
                </element>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsampling with specifying size-->
            <param name="otu" value="amazon.mothur.shared" ftype="mothur.shared"/>
            <param name="use" value="yes"/>

                        <has_text text="forest"/>
                        <has_text text="pasture"/>
                    </assert_contents>
                </element>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

5:7c8b0d0d792a

        </conditional>
        <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
            <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"/>
        <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"/>

        <test><!-- test with defaults -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output_collection name="distfiles" count="72">
                <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label,group select and all calculators -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.05,0.22"/>
            <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,structeuclidean,structpearson,sharednseqs,sharedobserved"/>
            <output_collection name="distfiles" count="74">
                <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsampling without specifying size -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.03,0.33"/>

                        <has_text text="forest"/>
                        <has_text text="pasture"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsampling with specifying size-->
            <param name="otu" value="amazon.mothur.shared" ftype="mothur.shared"/>
            <param name="use" value="yes"/>

                        <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[