From bf5bfd7cb17fb53a4bb1c197b6b00416f07cf559 Mon Sep 17 00:00:00 2001
From: Yi Zhang <yizhang@bx.psu.edu>
Date: Tue, 8 May 2007 18:36:31 +0000
Subject: [PATCH] Limit input files format of tool msbar, needle, newcpgseek to
 fasta

---
 tools/emboss/emboss_msbar.xml      | 11 +++++++++--
 tools/emboss/emboss_needle.xml     |  4 ++--
 tools/emboss/emboss_newcpgseek.xml | 11 +++++++++--
 3 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/tools/emboss/emboss_msbar.xml b/tools/emboss/emboss_msbar.xml
index 9ce9bc205a6..387cae48aa6 100644
--- a/tools/emboss/emboss_msbar.xml
+++ b/tools/emboss/emboss_msbar.xml
@@ -3,7 +3,7 @@
   <command>msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1
   -auto</command>
   <inputs>
-    <param format="data" name="input1" type="data">
+    <param format="fasta" name="input1" type="data">
       <label>Sequence 1</label>
     </param>
     <param name="count" size="4" type="text" value="1">
@@ -88,8 +88,15 @@
   </outputs>
   <code file="emboss_format_corrector.py" />
   <help>
+
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
     You can view the original documentation here_.
     
     .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/msbar.html
   </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/emboss/emboss_needle.xml b/tools/emboss/emboss_needle.xml
index ec63e98e519..13573611757 100644
--- a/tools/emboss/emboss_needle.xml
+++ b/tools/emboss/emboss_needle.xml
@@ -2,10 +2,10 @@
   <description>Needleman-Wunsch global alignment</description>
   <command>needle -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto</command>
   <inputs>
-    <param format="data" name="input1" type="data">
+    <param format="fasta" name="input1" type="data">
       <label>Sequence 1</label>
     </param>
-    <param format="data" name="input2" type="data">
+    <param format="fasta" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
     <param name="gapopen" size="4" type="text" value="10.0">
diff --git a/tools/emboss/emboss_newcpgseek.xml b/tools/emboss/emboss_newcpgseek.xml
index c88a8532c57..d71da957ee0 100644
--- a/tools/emboss/emboss_newcpgseek.xml
+++ b/tools/emboss/emboss_newcpgseek.xml
@@ -2,7 +2,7 @@
   <description>Reports CpG rich region</description>
   <command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command>
   <inputs>
-    <param format="data" name="input1" type="data">
+    <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
     <param name="score" size="4" type="text" value="17">
@@ -13,8 +13,15 @@
     <data format="txt" name="out_file1" />
   </outputs>
   <help>
+
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
     You can view the original documentation here_.
     
     .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/newcpgseek.html
   </help>
-</tool>
\ No newline at end of file
+</tool>