Mercurial > repos > iuc > mothur_dist_shared
diff dist.shared.xml @ 0:e478ba802667 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
| author | iuc |
|---|---|
| date | Fri, 24 Jun 2016 16:30:09 -0400 |
| parents | |
| children | 566e0fba8f4b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dist.shared.xml Fri Jun 24 16:30:09 2016 -0400 @@ -0,0 +1,164 @@ +<tool profile="16.07" id="mothur_dist_shared" name="Dist.shared" version="@WRAPPER_VERSION@.0"> + <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</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 'dist.shared( + shared=otu.dat, + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $groups: + groups=${ str($groups).replace(",","-") }, + #end if + #if $calc: + calc=${ str($calc).replace(",","-") }, + #end if + #if $subsampling.use == "yes": + #if $subsampling.subsample: + subsample=$subsampling.subsample, + #end if + iters=$subsampling.iters, + #end if + output=$output, + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + ]]></command> + <inputs> + <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> + <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> + <expand macro="labeloptions"/> + </param> + <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> + <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> + <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> + <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> + <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> + <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> + <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> + <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> + <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> + <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> + <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> + <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> + <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> + <option value="hamming">hamming - Community Membership Similarity -</option> + <option value="memchi2">memchi2 - Community Membership Similarity -</option> + <option value="memchord">memchord - Community Membership Similarity -</option> + <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option> + <option value="mempearson">mempearson - Community Membership Similarity -</option> + <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> + <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> + <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> + <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> + <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> + <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> + <option value="canberra">canberra - Community Structure Similarity -</option> + <option value="gower">gower - Community Structure Similarity -</option> + <option value="hellinger">hellinger - Community Structure Similarity -</option> + <option value="manhattan">manhattan - Community Structure Similarity -</option> + <option value="odum">odum - Community Structure Similarity -</option> + <option value="soergel">soergel - Community Structure Similarity -</option> + <option value="spearman">spearman - Community Structure Similarity -</option> + <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option> + <option value="structchi2">structchi2 - Community Structure Similarity -</option> + <option value="structchord">structchord - Community Structure Similarity -</option> + <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option> + <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option> + <option value="structpearson">structpearson - Community Structure Similarity -</option> + <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> + <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> + </param> + <conditional name="subsampling"> + <param name="use" type="select" label="subsample"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/> + <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> + </when> + <when value="no"/> + </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<designation>.*)\.dist" format="mothur.dist"/> + </collection> + </outputs> + <tests> + <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 --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="use" value="yes"/> + <param name="subsample" value="10"/> + <param name="iters" value="42"/> + <param name="label" value="0.03,0.33"/> + <param name="calc" value="canberra"/> + <param name="output" value="square"/> + <output_collection name="distfiles" count="6"> + <element name="canberra.0.33.square.std" ftype="mothur.dist"> + <assert_contents> + <has_text text="forest"/> + <has_text text="pasture"/> + </assert_contents> + </element> + </output_collection> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators + +.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _shared: http://www.mothur.org/wiki/Shared_file +.. _dist.shared: http://www.mothur.org/wiki/Dist.shared + +v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. + +]]> + </help> + <expand macro="citations"/> +</tool>