# HG changeset patch
# User jjohnson
# Date 1307563364 18000
# Node ID 5265aa9067e0da7ec077cdedd7bebeefe7374216
# Parent  b849cd7e132ab9b76f1e71633beb0cb52742c260
set output formats to match input formats

diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/bin.seqs.xml
--- a/mothur/tools/mothur/bin.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/bin.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -6,7 +6,7 @@
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 
-  --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:fasta'
+  --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}'
   --fasta=$fasta
   --list=$otu
   #if $name.__str__ != "None" and len($name.__str__) > 0:
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/bootstrap.shared.xml
--- a/mothur/tools/mothur/bootstrap.shared.xml	Wed Jun 08 14:59:08 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-<tool id="mothur_bootstrap_shared" name="Bootstrap.shared" version="1.16.0" force_history_refresh="True">
- <description>Generate a newick trees for dissimilarity among groups</description>
- <command interpreter="python">
-  #*
-98_sq_phylip_amazon.fn.jclass.bootunique.tre
-98_sq_phylip_amazon.fn.thetayc.bootunique.tre
-98_sq_phylip_amazon.fn.jclass.bootunique.cons.pairs
-98_sq_phylip_amazon.fn.jclass.bootunique.cons.tre
-98_sq_phylip_amazon.fn.thetayc.bootunique.cons.pairs
-98_sq_phylip_amazon.fn.thetayc.bootunique.cons.tre
-98_sq_phylip_amazon.fn.jclass.boot0.00.tre
-98_sq_phylip_amazon.fn.thetayc.boot0.00.tre
-98_sq_phylip_amazon.fn.jclass.boot0.00.cons.pairs
-98_sq_phylip_amazon.fn.jclass.boot0.00.cons.tre
-98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.pairs
-98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.tre
-  *#
-  mothur_wrapper.py 
-  --cmd='bootstrap.shared'
-  --result='^mothur.\S+\.logfile$:'$logfile
-  --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.pairs)$:txt'
-  --READ_cmd='read.otu'
-  #if $input.source == 'similarity':
-   --READ_list=$input.otu
-   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
-    --READ_group='$otu_group'
-   #end if
-   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
-   #end if
-  #elif $input.source == 'shared':
-   --READ_shared=$input.otu
-   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
-   #end if
-  #end if
-  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-   --groups=$input.groups
-  #end if
-  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
-   --calc=$calc
-  #end if
-  #if int($iters.__str__) > 0:
-   --iters=$iters
-  #end if
- </command>
- <inputs>
-  <!-- list,group  or shared -->
-  <conditional name="input">
-   <param name="source" type="select" label="Generate Heatmap for">
-    <option value="similarity">OTU list</option>
-    <option value="shared">OTU Shared</option>
-   </param>
-   <when value="similarity">
-     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
-     <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
-     <param name="label" type="select" label="label - OTU Labels" multiple="true">
-      <options from_dataset="otu">
-       <column name="name" index="0"/>
-       <column name="value" index="0"/>
-      </options>
-     </param>
-     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
-      <options from_dataset="otu_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="shared">
-     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
-     <param name="label" type="select" label="label - OTU Labels" multiple="true">
-      <options from_dataset="otu">
-       <column name="name" index="0"/>
-       <column name="value" index="0"/>
-       <filter type="unique_value" name="unq_lbl" column="0" />
-      </options>
-     </param>
-     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
-      <options from_dataset="otu">
-       <column name="name" index="1"/>
-       <column name="value" index="1"/>
-       <filter type="unique_value" name="unq_grp" column="1" />
-      </options>
-     </param>
-   </when>
-  </conditional>
-  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult2" index="2"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult2" column="2" value="shar" />
-   </options>
-  </param>
-  <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
- </inputs>
- <outputs>
-  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
- </outputs>
- <requirements>
-  <requirement type="binary">mothur</requirement>
- </requirements>
- <tests>
- </tests>
- <help>
-**Mothur Overview**
-
-Mothur_, initiated by Dr. Patrick Schloss and his software development team
-in the Department of Microbiology and Immunology at The University of Michigan,
-provides bioinformatics for the microbial ecology community.
-
-.. _Mothur: http://www.mothur.org/wiki/Main_Page
-
-**Command Documenation**
-
-The bootstrap.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.
-
-.. _bootstrap.shared: http://www.mothur.org/wiki/Bootstrap.shared
-
-
- </help>
-</tool>
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/cluster.fragments.xml
--- a/mothur/tools/mothur/cluster.fragments.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/cluster.fragments.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -25,7 +25,7 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
+  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
   <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
  </outputs>
  <requirements>
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/consensus.seqs.xml
--- a/mothur/tools/mothur/consensus.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/consensus.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -15,13 +15,13 @@
    #end if
    --result='^mothur.\S+\.logfile$:'$logfile
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-   --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:fasta','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular'
+   --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:${fasta.ext}','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular'
   #else
    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta
   #end if
  </command>
  <inputs>
-  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin" help="Sequences must be the same length"/>
+  <param name="fasta" type="data" format="align" label="fasta - Sequences to Bin" help="Sequences must be the same length"/>
   <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
   <conditional name="otu">
    <param name="use" type="select" label="Consensus sequence">
@@ -45,7 +45,7 @@
   <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary">
    <filter>otu['use'] == 'no'</filter>
   </data>
-  <data format="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta">
+  <data format_source="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta">
    <filter>otu['use'] == 'no'</filter>
   </data>
  </outputs>
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/degap.seqs.xml
--- a/mothur/tools/mothur/degap.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/degap.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -12,7 +12,7 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
+  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/deunique.seqs.xml
--- a/mothur/tools/mothur/deunique.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/deunique.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -14,7 +14,7 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
+  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/get.groups.xml
--- a/mothur/tools/mothur/get.groups.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/get.groups.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -52,7 +52,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/>
   <!-- fix format -->
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
+  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
    <filter>fasta_in != None</filter>
   </data>
   <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name">
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/get.lineage.xml
--- a/mothur/tools/mothur/get.lineage.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/get.lineage.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -53,7 +53,7 @@
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/>
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
+  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
    <filter>fasta_in != None</filter>
   </data>
   <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group">
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/get.oturep.xml
--- a/mothur/tools/mothur/get.oturep.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/get.oturep.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -7,7 +7,7 @@
   --outputdir='$logfile.extra_files_path'
   #if $as_datasets.__str__ == "yes":
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-   --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
+   --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
   #end if
   --fasta=$fasta
   --list=$otu_list
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/get.seqs.xml
--- a/mothur/tools/mothur/get.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/get.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -53,11 +53,11 @@
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <!-- format should be set to match input -->
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
+  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
    <filter>fasta_in != None</filter>
   </data>
   <!-- format should be set to match input -->
-  <data format="qual" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile">
+  <data format_source="qfile_in" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile">
    <filter>qfile_in != None</filter>
   </data>
   <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names">
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/get.sharedseqs.xml
--- a/mothur/tools/mothur/get.sharedseqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/get.sharedseqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -23,7 +23,7 @@
   #end if
   #if $fasta.__str__ != "None" and len($fasta.__str__) > 0:
    --fasta=$fasta
-   #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.fasta)$:fasta'"]
+   #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.fasta)$:" + $fasta.ext + "'"]
   #end if
   #if $output.__str__ != "None" and len($output.__str__) > 0:
    --output=$output
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/pre.cluster.xml
--- a/mothur/tools/mothur/pre.cluster.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/pre.cluster.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -25,7 +25,7 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: precluster.fasta" />
+  <data format_source="fasta" name="fasta_out" label="${tool.name} on ${on_string}: precluster.fasta" />
   <data format="names" name="names_out" label="${tool.name} on ${on_string}: precluster.names" />
  </outputs>
  <requirements>
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/read.otu.xml
--- a/mothur/tools/mothur/read.otu.xml	Wed Jun 08 14:59:08 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-<tool id="mothur_read_otu" name="Read.otu" version="1.16.0" force_history_refresh="True">
- <description>Read OTU list and group to create a shared file</description>
- <command interpreter="python">
-  mothur_wrapper.py 
-  --cmd='read.otu'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared:'$shared
-  --outputdir='$logfile.extra_files_path'
-  #if $show_rabund.value == True:
-   --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 
-   --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund'
-  #end if
-  --list=$otu
-  --group=$otu_group
-  #if $label.__str__ != "None" and len($label.__str__) > 0:
-   --label='$label'
-  #end if
- </command>
- <inputs>
-  <param name="otu" type="data" format="list" label="list - OTU List"/>
-  <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/>
-  <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
-   <options from_dataset="otu">
-    <column name="name" index="0"/>
-    <column name="value" index="0"/>
-   </options>
-  </param>
-  <param name="show_rabund" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Put Group rabund files in your history"/>
- </inputs>
- <outputs>
-  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" />
- </outputs>
- <requirements>
-  <requirement type="binary">mothur</requirement>
- </requirements>
- <tests>
- </tests>
- <help>
-**Mothur Overview**
-
-Mothur_, initiated by Dr. Patrick Schloss and his software development team
-in the Department of Microbiology and Immunology at The University of Michigan,
-provides bioinformatics for the microbial ecology community.
-
-.. _Mothur: http://www.mothur.org/wiki/Main_Page
-
-**Command Documenation**
-
-The read.otu_ command is called before most of the OTU based mothur commands.  It is included here explicitly to allow the creatation of a shared file from OTU list and group files.  
-
-.. _read.otu: http://www.mothur.org/wiki/Read.otu
-
- </help>
-</tool>
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/remove.lineage.xml
--- a/mothur/tools/mothur/remove.lineage.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/remove.lineage.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -54,7 +54,7 @@
   <!-- fix format -->
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/>
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
+  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
    <filter>fasta_in != None</filter>
   </data>
   <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group">
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/remove.seqs.xml
--- a/mothur/tools/mothur/remove.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/remove.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -58,14 +58,14 @@
    <filter>fasta_in != None</filter>
   </data>
   -->
-  <data format="fasta" metadata_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.${fasta_in.datatype.file_ext}">
+  <data format_source="fasta_in" metadata_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.${fasta_in.datatype.file_ext}">
    <filter>fasta_in != None</filter>
    <change_format>
      <when input="${fasta_in.datatype.file_ext}" value="align" format="align" />
    </change_format>
   </data>
   <!-- format should be set to match input -->
-  <data format="qual" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile">
+  <data format_source="qfile_in" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile">
    <filter>qfile_in != None</filter>
    <change_format>
      <when input="${qfile_in.datatype.file_ext}" value="qual454" format="qual454" />
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/split.abund.xml
--- a/mothur/tools/mothur/split.abund.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/split.abund.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -10,10 +10,10 @@
   #set datasets = []
   #if $as_datasets.__str__ == "yes":
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-   --new_datasets='^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.fasta)$:fasta','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.groups)$:groups','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.accnos)$:accnos'
+   --new_datasets='^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.groups)$:groups','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.accnos)$:accnos'
   #end if
   --fasta=$fasta
-  #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.fasta)$',$os.path.basename($fasta.__str__)) + ":fasta'"]
+  #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.fasta)$',$os.path.basename($fasta.__str__)) + ":" + $fasta.ext + "'"]
   #if $search.type == "list":
    --list=$search.input
    #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.list)$',$os.path.basename($search.input.__str__)) + ":list'"]
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/split.groups.xml
--- a/mothur/tools/mothur/split.groups.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/split.groups.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -6,7 +6,7 @@
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.names)$:names'
+  --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.names)$:names'
   --fasta=$fasta
   --group=$group
   #if $name.__str__ != "None" and len($name.__str__) > 0:
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/sub.sample.xml
--- a/mothur/tools/mothur/sub.sample.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/sub.sample.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -165,7 +165,7 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: subsample.fasta">
+  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: subsample.fasta">
    <filter>input['format'] == 'fasta'</filter>
   </data>
   <data format="list" name="list_out" label="${tool.name} on ${on_string}: subsample.list">
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/trim.seqs.xml
--- a/mothur/tools/mothur/trim.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/trim.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -37,7 +37,7 @@
    $oligo.allfiles
    #if $oligo.allfiles.value:
     --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-    --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.groups)$:groups'
+    --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.groups)$:groups'
    #end if
   #end if
   #if $qual.add == "yes":
@@ -95,11 +95,11 @@
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format_source="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/>
-  <data format="qual" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual">
+  <data format_source="qfile" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual">
    <filter>(qual['add'] == 'yes'  and len(qual['qfile'].__str__) > 0)</filter>
   </data>
-  <data format="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/>
-  <data format="qual" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual">
+  <data format_source="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/>
+  <data format_source="qfile" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual">
    <filter>(qual['add'] == 'yes'  and len(qual['qfile'].__str__) > 0)</filter>
   </data>
   <data format="groups" name="groups_file" label="${tool.name} on ${on_string}: groups">
diff -r b849cd7e132a -r 5265aa9067e0 mothur/tools/mothur/unique.seqs.xml
--- a/mothur/tools/mothur/unique.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
+++ b/mothur/tools/mothur/unique.seqs.xml	Wed Jun 08 15:02:44 2011 -0500
@@ -16,7 +16,7 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
+  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
   <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
  </outputs>
  <requirements>