diff mothur/README @ 15:a6189f58fedb

Mothur - updated for Mothur version 1.22.0

--- a/mothur/README	Wed Oct 05 10:37:11 2011 -0500
+++ b/mothur/README	Tue Nov 08 11:45:32 2011 -0600
@@ -1,7 +1,9 @@
 Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 
 
-Install mothur v.1.20.0 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 )
+(The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
+
+Install mothur v.1.22.0 on your galaxy system so galaxy can execute the mothur command
+  ( This version of wrappers is designed for Mothur version 1.22 - it may work on later versions )
   http://www.mothur.org/wiki/Download_mothur
   http://www.mothur.org/wiki/Installation
   ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
@@ -45,6 +47,8 @@
   SILVA-compatible mask:
      - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
        http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
+ Lookup Files for sff flow analysis using shhh.flows:
+  http://www.mothur.org/wiki/Alignment_database
 
  Example from UMN installation: (We also made these available in a Galaxy public data library)
     /project/db/galaxy/mothur/Silva.bacteria.zip
@@ -117,6 +121,9 @@
         <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="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
+            <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
+        </datatype>
         <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"/>
@@ -127,6 +134,7 @@
         <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="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
         <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
         <!-- End Mothur Datatypes -->
 
@@ -138,10 +146,13 @@
       <tool file="mothur/get.groups.xml"/>
       <tool file="mothur/remove.groups.xml"/>
       <tool file="mothur/merge.groups.xml"/>
+      <tool file="mothur/count.groups.xml"/>
       <tool file="mothur/make.design.xml"/>
       <tool file="mothur/sub.sample.xml"/>
     <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
       <tool file="mothur/sffinfo.xml"/>
+      <tool file="mothur/trim.flows.xml"/>
+      <tool file="mothur/shhh.flows.xml"/>
       <tool file="mothur/make.fastq.xml"/>
       <tool file="mothur/fastq.info.xml"/>
       <tool file="mothur/summary.seqs.xml"/>
@@ -169,6 +180,7 @@
       <tool file="mothur/nmds.xml"/>
       <tool file="mothur/corr.axes.xml"/>
       <tool file="mothur/classify.seqs.xml"/>
+      <tool file="mothur/seq.error.xml"/>
     <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
       <tool file="mothur/chimera.bellerophon.xml"/>
       <tool file="mothur/chimera.ccode.xml"/>
@@ -200,6 +212,7 @@
       <tool file="mothur/get.group.xml"/>
       <tool file="mothur/bin.seqs.xml"/>
       <tool file="mothur/get.sharedseqs.xml"/>
+      <tool file="mothur/summary.tax.xml"/>
     <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
       <tool file="mothur/collect.single.xml"/>
       <tool file="mothur/rarefaction.single.xml"/>
@@ -235,10 +248,11 @@
       <tool file="mothur/TreeVector.xml"/>
   </section> <!-- metagenomics_mothur -->
 
-
 ############ DESIGN NOTES #########################################################################################################
 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
 
+  (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
+
 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
 * Every tool will produce the logfile of the mothur run as an output.
 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py