diff mothur/tools/mothur/remove.groups.xml @ 12:370b3fc4e7d3

Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings

--- a/mothur/tools/mothur/remove.groups.xml	Thu Jul 14 15:21:01 2011 -0500
+++ b/mothur/tools/mothur/remove.groups.xml	Tue Aug 09 11:39:27 2011 -0500
@@ -1,4 +1,4 @@
-<tool id="mothur_remove_groups" name="Remove.groups" version="1.19.0">
+<tool id="mothur_remove_groups" name="Remove.groups" version="1.21.0">
  <description>Remove groups from groups,fasta,names,list,taxonomy</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -20,22 +20,25 @@
   #end if
   #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
    --fasta=$fasta_in
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__]
   #end if
   #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
    --name=$name_in
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
   #end if
   #if $list_in.__str__ != "None" and len($list_in.__str__) > 0:
    --list=$list_in
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
+  #end if
+  #if $shared_in.__str__ != "None" and len($shared_in.__str__) > 0:
+   --shared=$shared_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($shared_in.__str__)) + ":'" + $shared_out.__str__]
   #end if
   #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0:
    --taxonomy=$taxonomy_in
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
   #end if
   --result=#echo ','.join($results)
-
  </command>
  <inputs>
   <param name="group_in" type="data" format="groups" label="group - Groups"/>
@@ -60,6 +63,7 @@
   <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/>
   <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
   <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
+  <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/>
   <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
  </inputs>
  <outputs>
@@ -75,6 +79,9 @@
   <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
    <filter>list_in != None</filter>
   </data>
+  <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared">
+   <filter>shared_in != None</filter>
+  </data>
   <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
    <filter>taxonomy_in != None</filter>
   </data>