diff mothur/tools/mothur/phylo.diversity.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

--- a/mothur/tools/mothur/phylo.diversity.xml	Mon Jun 27 09:34:14 2011 -0500
+++ b/mothur/tools/mothur/phylo.diversity.xml	Mon Jun 27 10:12:25 2011 -0500
@@ -1,4 +1,4 @@
-<tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.19.0">
+<tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.20.0">
  <description>Alpha Diversity calculates unique branch length</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -6,11 +6,13 @@
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.phylodiv\.summary$:'$summary_out,'^\S+\.phylodiv$:'$collectors_out,'^\S+\.rarefaction$:'$rarefaction_out
   --outputdir='$logfile.extra_files_path'
   --tree=$tree
-  #if $group.__str__ != "None" and len($group.__str__) > 0:
-   --group='$group'
-  #end if
-  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
-   --groups='$groups'
+  #if $grouping.use:
+   #if $grouping.group.__str__ != "None" and len($grouping.group.__str__) > 0:
+    --group='$grouping.group'
+   #end if
+   #if $grouping.groups.__str__ != "None" and len($grouping.groups.__str__) > 0:
+    --groups='$grouping.groups'
+   #end if
   #end if
   #if $name.__str__ != "None" and len($name.__str__) > 0:
    --name='$name'
@@ -32,14 +34,21 @@
  <inputs>
   <!-- list,group  or shared -->
   <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/>
-  <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
-  <param name="groups" type="select" label="groups - Groups to display" multiple="true">
-   <options from_dataset="group">
-    <column name="name" index="1"/>
-    <column name="value" index="1"/>
-    <filter type="unique_value" name="unq_grp" column="1" />
-   </options>
-  </param>
+  <conditional name="grouping">
+   <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Analyze by group using a Group file"/>
+   <when value="yes">
+   <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
+   <param name="groups" type="select" label="groups - Groups to display" multiple="true">
+    <help>All groups displayed if none are selected.</help>
+    <options from_dataset="group">
+     <column name="name" index="1"/>
+     <column name="value" index="1"/>
+     <filter type="unique_value" name="unq_grp" column="1" />
+    </options>
+   </param>
+   </when>
+   <when value="no"/>
+  </conditional> <!-- use_groups -->
   <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/>
   <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
   <param name="freq" type="float" value="0.0" label="freq - Reporting frequency"