Mercurial > repos > iuc > mothur_get_communitytype
view get.communitytype.xml @ 8:79dc573692a4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author | iuc |
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date | Tue, 08 Dec 2020 15:16:37 +0000 |
parents | beb4e0832f3b |
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<tool profile="16.07" id="mothur_get_communitytype" name="Get.communitytype" version="@WRAPPER_VERSION@.0"> <description>description</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' shared.dat && echo 'get.communitytype( shared=shared.dat, #if $label: label=${ str($label).replace(",","-") }, #end if #if $groups: groups=${ str($groups).replace(",","-") }, #end if method=$m.method, #if $m.method == 'kmeans' or $m.method == 'pams': calc=$m.calc, iters=$m.iters, #end if #if int($subsample) == 0: subsample=T, #elif int($subsample) > 0: subsample=$subsample, #end if minpartitions=$minpartitions, maxpartitions=$maxpartitions, optimizegap=$optimizegap, 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 - Shared file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true"> <expand macro="labeloptions"/> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true" optional="true"> <options> <filter type="data_meta" ref="otu" key="groups"/> </options> </param> <conditional name="m"> <param name="method" type="select" label="method"> <option value="dmm" selected="true">dmm</option> <option value="kmeans">k means</option> <option value="pam">pam</option> </param> <when value="dmm"/> <when value="kmeans"> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)"> <expand macro="calc-common"/> <!-- set default option(s) --> <option value="rjsd" selected="true">rjsd</option> </param> <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/> </when> <when value="pam"> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)"> <expand macro="calc-common"/> <!-- set default option --> <option value="rjsd" selected="true">rjsd</option> </param> <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/> </when> </conditional> <param name="minpartitions" type="integer" value="5" min="0" label="minpartitions" help=""/> <param name="maxpartitions" type="integer" value="10" min="0" label="minpartitions" help=""/> <param name="optimizegap" type="integer" value="3" min="0" label="minpartitions" help=""/> <param name="subsample" type="integer" value="-1" min="-1" label="subsample" help="Ignored if negative, when set to 0 it uses the size of your smallest group (subsample=T)"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="summary" format="tabular" from_work_dir="shared*.summary" label="${tool.name} on ${on_string}: summary"> <filter> m['method'] == 'dmm' </filter> </data> <data name="design" format="tabular" from_work_dir="shared*.design" label="${tool.name} on ${on_string}: design"/> <data name="parameters" format="tabular" from_work_dir="shared*.parameters" label="${tool.name} on ${on_string}: parameters"> <filter> m['method'] == 'dmm' </filter> </data> <data name="fit" format="tabular" from_work_dir="shared*.fit" label="${tool.name} on ${on_string}: fit"/> <collection name="relabund" type="list" label="${tool.name} on ${on_string}: relabund"> <discover_datasets pattern="shared\.(?P<designation>.*)\.relabund" format="mothur.relabund"/> </collection> <collection name="posterior" type="list" label="${tool.name} on ${on_string}: posterior"> <discover_datasets pattern="shared\.(?P<designation>.*)\.posterior" format="tabular"/> </collection> </outputs> <tests> <test><!-- test with defaults --> <param name="otu" value="final.tx.1.subsample.1.pick.shared"/> <output name="summary" md5="3e81c01da5f6c86b69516e204ad51610" ftype="tabular"/> <output name="design" md5="df00e5ea21154669bbb85efa20a9661d" ftype="tabular"/> <output name="parameters" md5="ef972523811b80b12d4343f0df472214" ftype="tabular"/> <output name="fit" ftype="tabular"> <assert_contents> <has_line_matching expression="K\tNLE\tlogDet\tBIC\tAIC\tLaplace"/> </assert_contents> </output> <output_collection name="relabund" count="5"> <element name="1.dmm.1.mix" md5="9c338b1fb5aea4baae2dbf242331d27c" ftype="mothur.relabund"/> </output_collection> <output_collection name="posterior" count="5"> <element name="1.dmm.1.mix" md5="fae04096d53d6980d8eb712e6ec8b0d2" ftype="tabular"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with all settings --> <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/> <param name="label" value="1"/> <param name="groups" value="F003D000,F003D002,F003D006,F003D008,F003D142"/> <param name="method" value="kmeans"/> <param name="iters" value="100"/> <param name="calc" value="manhattan"/> <param name="maxpartitions" value="4"/> <param name="subsample" value="0"/> <output name="design" ftype="tabular"> <assert_contents> <has_text text="Partition_"/> <has_text text="F003D000"/> <has_text text="F003D142"/> </assert_contents> </output> <output name="fit" ftype="tabular"> <assert_contents> <has_line_matching expression="K\tCH\tF003D000\tF003D002\tF003D006\tF003D008\tF003D142"/> </assert_contents> </output> <output_collection name="relabund" count="4"> <element name="1.kmeans.1.mix" md5="514780678b8d9413566df3355d427e27" ftype="mothur.relabund"/> </output_collection> <output_collection name="posterior" count="4"> <element name="1.kmeans.1.mix" md5="43f4dfc2bcd1cf20db4f89ee90b6041c" ftype="tabular"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** .. _get.communitytype: https://www.mothur.org/wiki/Get.communitytype ]]></help> <expand macro="citations"> <citation type="doi">10.1371/journal.pone.0030126</citation> </expand> </tool>