Mercurial > repos > iuc > mothur_dist_shared
diff dist.shared.xml @ 1:566e0fba8f4b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 04:36:19 -0400 |
| parents | e478ba802667 |
| children | 3257183be791 |
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--- a/dist.shared.xml Fri Jun 24 16:30:09 2016 -0400 +++ b/dist.shared.xml Fri May 19 04:36:19 2017 -0400 @@ -4,8 +4,11 @@ <import>macros.xml</import> </macros> <expand macro="requirements"/> + <expand macro="stdio"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ + <command><![CDATA[ + @SHELL_OPTIONS@ + ## create symlinks to input datasets ln -s "$otu" otu.dat && @@ -31,6 +34,7 @@ )' | 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"/> @@ -43,46 +47,10 @@ </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> + <expand macro="calc-common"/> + <!-- set default option(s) --> <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"> @@ -148,13 +116,13 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** -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 +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: https://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 +.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _shared: https://www.mothur.org/wiki/Shared_file +.. _dist.shared: https://www.mothur.org/wiki/Dist.shared v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.