Mercurial > repos > jjohnson > mothur_toolsuite

diff mothur/README @ 2:e990ac8a0f58

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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:39:06 -0400
parents fcc0778f6987
children 7bfe1f843858
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line diff
--- a/mothur/README	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/README	Tue Jun 07 17:39:06 2011 -0400
@@ -1,9 +1,10 @@
 Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 
 
-Install mothur v.1.16.0 on your galaxy system so galaxy can execute the mothur command
+Install mothur v.1.19.0 on your galaxy system so galaxy can execute the mothur command
+  ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions )
   http://www.mothur.org/wiki/Download_mothur
   http://www.mothur.org/wiki/Installation
-  ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
+  ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
 
 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
   TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
@@ -102,11 +103,13 @@
         <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
         <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
         <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
+        <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
         <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
         <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
         <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
         <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
         <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
+        <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/>
         <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
         <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
         <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
@@ -114,7 +117,8 @@
         <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
         <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
         <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
-        <datatype extension="taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
+        <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
+        <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
         <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
         <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
         <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
@@ -122,6 +126,7 @@
         <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
         <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
         <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
+        <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
         <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
         <!-- End Mothur Datatypes -->
 
@@ -137,6 +142,7 @@
       <tool file="mothur/sub.sample.xml"/>
     <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
       <tool file="mothur/sffinfo.xml"/>
+      <tool file="mothur/make.fastq.xml"/>
       <tool file="mothur/fastq.info.xml"/>
       <tool file="mothur/summary.seqs.xml"/>
       <tool file="mothur/reverse.seqs.xml"/>
@@ -162,7 +168,7 @@
       <tool file="mothur/nmds.xml"/>
       <tool file="mothur/corr.axes.xml"/>
       <tool file="mothur/classify.seqs.xml"/>
-   <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
+    <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
       <tool file="mothur/chimera.bellerophon.xml"/>
       <tool file="mothur/chimera.ccode.xml"/>
       <tool file="mothur/chimera.check.xml"/>
@@ -176,15 +182,22 @@
       <tool file="mothur/cluster.classic.xml"/>
       <tool file="mothur/cluster.split.xml"/>
       <tool file="mothur/metastats.xml"/>
-      <tool file="mothur/read.otu.xml"/>
+      <tool file="mothur/sens.spec.xml"/>
       <tool file="mothur/classify.otu.xml"/>
       <tool file="mothur/parse.list.xml"/>
       <tool file="mothur/get.otus.xml"/>
       <tool file="mothur/remove.otus.xml"/>
       <tool file="mothur/remove.rare.xml"/>
+      <tool file="mothur/get.otulist.xml"/>
       <tool file="mothur/get.oturep.xml"/>
+      <tool file="mothur/otu.hierarchy.xml"/>
+      <tool file="mothur/get.rabund.xml"/>
+      <tool file="mothur/get.sabund.xml"/>
       <tool file="mothur/get.relabund.xml"/>
+      <tool file="mothur/make.shared.xml"/>
       <tool file="mothur/get.group.xml"/>
+      <tool file="mothur/bin.seqs.xml"/>
+      <tool file="mothur/get.sharedseqs.xml"/>
     <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
       <tool file="mothur/collect.single.xml"/>
       <tool file="mothur/rarefaction.single.xml"/>
@@ -205,6 +218,10 @@
       <tool file="mothur/unifrac.weighted.xml"/>
       <tool file="mothur/unifrac.unweighted.xml"/>
       <tool file="mothur/libshuff.xml"/>
+      <tool file="mothur/amova.xml"/>
+      <tool file="mothur/homova.xml"/>
+      <tool file="mothur/mantel.xml"/>
+      <tool file="mothur/anosim.xml"/>
     <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
       <tool file="mothur/get.lineage.xml"/>
       <tool file="mothur/remove.lineage.xml"/>
@@ -212,7 +229,6 @@
       <tool file="mothur/phylo.diversity.xml"/>
       <tool file="mothur/clearcut.xml"/>
       <tool file="mothur/indicator.xml"/>
-      <tool file="mothur/bootstrap.shared.xml"/>
       <tool file="mothur/TreeVector.xml"/>
   </section> <!-- metagenomics_mothur -->