# HG changeset patch
# User jj@dbw-galaxy-dev.msi.umn.edu
# Date 1307563148 18000
# Node ID b849cd7e132ab9b76f1e71633beb0cb52742c260
# Parent  e990ac8a0f58f0c7f89b3d901c82c4916378222f
workflow cleanup_param_values recurses through paramnames whenever they start with a paramname_, so change input to input_fasta

diff -r e990ac8a0f58 -r b849cd7e132a mothur/tools/mothur/screen.seqs.xml
--- a/mothur/tools/mothur/screen.seqs.xml	Tue Jun 07 17:39:06 2011 -0400
+++ b/mothur/tools/mothur/screen.seqs.xml	Wed Jun 08 14:59:08 2011 -0500
@@ -5,11 +5,11 @@
   #import re, os.path
   --cmd='screen.seqs'
   #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
-  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input.__str__)) + ":'" + $out_file.__str__]
-  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input.__str__)) + ":'" + $bad_accnos.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_fasta.__str__)) + ":'" + $out_file.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input_fasta.__str__)) + ":'" + $bad_accnos.__str__]
   --outputdir='$logfile.extra_files_path'
   --tmpdir='${logfile.extra_files_path}/input'
-  --fasta=$input
+  --fasta=$input_fasta
   #if int($start) >= 0:
    --start=$start
   #end if
@@ -54,7 +54,7 @@
   --processors=2
  </command>
  <inputs>
-  <param name="input" type="data" format="fasta,align" label="fasta - Fasta to screen"/>
+  <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/>
   <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
   <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
   <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
@@ -77,7 +77,7 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format_source="input" name="out_file" label="${tool.name} on ${on_string}: good.${input.datatype.file_ext}" />
+  <data format_source="input_fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input_fasta.datatype.file_ext}" />
   <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" />
   <data format_source="input_qfile" name="output_qfile" label="${tool.name} on ${on_string}: qfile" >
    <filter>input_qfile != None</filter>