From 5e3085d2585475fd4268c4776bfa27abbbe9ae03 Mon Sep 17 00:00:00 2001
From: Jianbin He <jbhe@bx.psu.edu>
Date: Tue, 13 Mar 2007 19:23:19 +0000
Subject: [PATCH] change the param name for toolbox test

---
 tools/filters/axt_to_concat_fasta.xml       | 6 +++---
 tools/filters/axt_to_fasta.xml              | 7 +++----
 tools/filters/ucsc_gene_bed_to_exon_bed.xml | 2 +-
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/tools/filters/axt_to_concat_fasta.xml b/tools/filters/axt_to_concat_fasta.xml
index f8ea67d9fb2..91b3e918360 100644
--- a/tools/filters/axt_to_concat_fasta.xml
+++ b/tools/filters/axt_to_concat_fasta.xml
@@ -1,9 +1,9 @@
 <tool id="axt_to_concat_fasta" name="AXT to concatenated FASTA">
     <description>Converts an AXT formated file to a concatenated FASTA alignment</description>
-    <command interpreter="python2.4">axt_to_concat_fasta.py $dbkey_1 $dbkey_2 &lt; $axt_file &gt; $out_file1</command>
+    <command interpreter="python2.4">axt_to_concat_fasta.py $dbkey_1 $dbkey_2 &lt; $axt_input &gt; $out_file1</command>
     <inputs>
         <page>
-            <param format="axt" name="axt_file" type="data" label="AXT file"/>
+            <param format="axt" name="axt_input" type="data" label="AXT file"/>
 
             <param label="Genome" name="dbkey_1" type="select" dynamic_options="get_available_builds()"/>
             <param label="Genome" name="dbkey_2" type="select" dynamic_options="get_available_builds()"/>
@@ -15,7 +15,7 @@
     </outputs>
     <tests>
       <test>
-        <param name="axt_file" value="1.axt" />
+        <param name="axt_input" value="1.axt" />
         <param name="dbkey_1" value='hg17' />
         <param name="dbkey_2" value="panTro1" />
         <output name="out_file1" file="axt_to_concat_fasta.dat" />
diff --git a/tools/filters/axt_to_fasta.xml b/tools/filters/axt_to_fasta.xml
index 09642fa6f5f..c3d44723742 100644
--- a/tools/filters/axt_to_fasta.xml
+++ b/tools/filters/axt_to_fasta.xml
@@ -1,10 +1,9 @@
 <tool id="axt_to_fasta" name="AXT to FASTA">
     <description>Converts an AXT formated file to FASTA format</description>
-    <command interpreter="python2.4">axt_to_fasta.py $dbkey_1 $dbkey_2 &lt; $axt_file &gt; $out_file1</command>
+    <command interpreter="python2.4">axt_to_fasta.py $dbkey_1 $dbkey_2 &lt; $axt_input &gt; $out_file1</command>
     <inputs>
         <page>
-            <param format="axt" name="axt_file" type="data" label="AXT file"/>
-
+            <param format="axt" name="axt_input" type="data" label="AXT file"/>
             <param label="Genome" name="dbkey_1" type="select" dynamic_options="get_available_builds()"/>
             <param label="Genome" name="dbkey_2" type="select" dynamic_options="get_available_builds()"/>
 
@@ -15,7 +14,7 @@
     </outputs>
     <tests>
       <test>
-        <param name="axt_file" value="1.axt" />
+        <param name="axt_input" value="1.axt" />
         <param name="dbkey_1" value='hg17' />
         <param name="dbkey_2" value="panTro1" />
         <output name="out_file1" file="axt_to_fasta.dat" />
diff --git a/tools/filters/ucsc_gene_bed_to_exon_bed.xml b/tools/filters/ucsc_gene_bed_to_exon_bed.xml
index a7e35682448..c0d091dd0de 100644
--- a/tools/filters/ucsc_gene_bed_to_exon_bed.xml
+++ b/tools/filters/ucsc_gene_bed_to_exon_bed.xml
@@ -2,7 +2,7 @@
 <description>expander</description>
   <command interpreter="python">ucsc_gene_bed_to_exon_bed.py --input=$input1 --output=$out_file1 --region=$region "--exons"</command>
   <inputs>
-    <param name="input1" type="data" format="interval" label="UCSC Gene Table"/>
+    <param name="input1" type="data" format="bed" label="UCSC Gene Table"/>
     <param name="region" type="select">
       <label>Feature Type</label>
       <option value="transcribed">Coding + UTR</option>