diff mothur/tools/mothur/remove.seqs.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/remove.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
+++ b/mothur/tools/mothur/remove.seqs.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_remove_seqs" name="Remove.seqs" version="1.15.0">
+<tool id="mothur_remove_seqs" name="Remove.seqs" version="1.16.0">
  <description>Remove sequences by name</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -41,8 +41,8 @@
  </command>
  <inputs>
   <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/>
-  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
-  <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
+  <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/>
+  <param name="qfile_in" type="data" format="qual,qual454" optional="true" label="qfile - Fasta Quality"/>
   <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
   <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/>
   <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/>
@@ -53,12 +53,23 @@
  <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 ${on_string}: pick.fasta">
+  <!-- There should be a  format_source   attribute
+  <data format_source="fasta_in" metadata_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.${fasta_in.datatype.file_ext}">
    <filter>fasta_in != None</filter>
   </data>
+  -->
+  <data format="fasta" 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 ${on_string}: pick.qfile">
    <filter>qfile_in != None</filter>
+   <change_format>
+     <when input="${qfile_in.datatype.file_ext}" value="qual454" format="qual454" />
+   </change_format>
   </data>
   <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names">
    <filter>name_in != None</filter>