diff mothur/tools/mothur/summary.shared.xml @ 19:d86987601022

Move calc options in individual tools and remove tool-data/mothur_calculators.loc

--- a/mothur/tools/mothur/summary.shared.xml	Tue Jan 17 11:22:44 2012 -0600
+++ b/mothur/tools/mothur/summary.shared.xml	Tue Jan 17 14:16:44 2012 -0600
@@ -40,12 +40,46 @@
    </options>
   </param>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult" index="1"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult" column="1" value="shared" />
-   </options>
+   <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+   <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+   <option value="sharedace" selected="true">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" selected="true">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" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+   <option value="sorest" selected="true">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" selected="true">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" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+   <option value="thetan" selected="true">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>
   <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
   <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Output a distance file for each calculator at each label"/>