From e1eedcab6021adb5c888a293dfa5e5b6faa7b841 Mon Sep 17 00:00:00 2001
From: Jianbin He <jbhe@bx.psu.edu>
Date: Tue, 13 Mar 2007 15:20:46 +0000
Subject: [PATCH] change keyword 'value' to 'file' for test_toolbox

---
 tools/filters/axt_to_concat_fasta.xml         | 2 +-
 tools/filters/axt_to_fasta.xml                | 2 +-
 tools/filters/bed2gff.xml                     | 2 +-
 tools/filters/gff2bed.xml                     | 2 +-
 tools/filters/ucsc_gene_bed_to_exon_bed.xml   | 2 +-
 tools/filters/ucsc_gene_bed_to_intron_bed.xml | 2 +-
 tools/stats/gsummary.xml                      | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tools/filters/axt_to_concat_fasta.xml b/tools/filters/axt_to_concat_fasta.xml
index 5309196f4a2..f8ea67d9fb2 100644
--- a/tools/filters/axt_to_concat_fasta.xml
+++ b/tools/filters/axt_to_concat_fasta.xml
@@ -18,7 +18,7 @@
         <param name="axt_file" value="1.axt" />
         <param name="dbkey_1" value='hg17' />
         <param name="dbkey_2" value="panTro1" />
-        <output name="out_file1" value="axt_to_concat_fasta.dat" />
+        <output name="out_file1" file="axt_to_concat_fasta.dat" />
       </test>
     </tests>
     <help>
diff --git a/tools/filters/axt_to_fasta.xml b/tools/filters/axt_to_fasta.xml
index 4778225de18..09642fa6f5f 100644
--- a/tools/filters/axt_to_fasta.xml
+++ b/tools/filters/axt_to_fasta.xml
@@ -18,7 +18,7 @@
         <param name="axt_file" value="1.axt" />
         <param name="dbkey_1" value='hg17' />
         <param name="dbkey_2" value="panTro1" />
-        <output name="out_file1" value="axt_to_fasta.dat" />
+        <output name="out_file1" file="axt_to_fasta.dat" />
       </test>
     </tests>
     <help>
diff --git a/tools/filters/bed2gff.xml b/tools/filters/bed2gff.xml
index 1bfbc13085f..ddc2c463fad 100644
--- a/tools/filters/bed2gff.xml
+++ b/tools/filters/bed2gff.xml
@@ -10,7 +10,7 @@
   <tests>
     <test>
       <param name="input" value="1.bed"/>
-      <output name="out_file1" value="cf-bed2gff.dat"/>
+      <output name="out_file1" file="cf-bed2gff.dat"/>
     </test>
   </tests>
   <help>
diff --git a/tools/filters/gff2bed.xml b/tools/filters/gff2bed.xml
index 81df2963bbc..770ef350da9 100644
--- a/tools/filters/gff2bed.xml
+++ b/tools/filters/gff2bed.xml
@@ -10,7 +10,7 @@
   <tests>
     <test>
       <param name="input" value="5.gff"/>
-      <output name="out_file1" value="cf-gff2bed.dat"/>
+      <output name="out_file1" file="cf-gff2bed.dat"/>
     </test>
   </tests>
   <help>
diff --git a/tools/filters/ucsc_gene_bed_to_exon_bed.xml b/tools/filters/ucsc_gene_bed_to_exon_bed.xml
index c2e5fd8a34f..a7e35682448 100644
--- a/tools/filters/ucsc_gene_bed_to_exon_bed.xml
+++ b/tools/filters/ucsc_gene_bed_to_exon_bed.xml
@@ -21,7 +21,7 @@
     <test>
       <param name="input1" value="3.bed" /> 
       <param name="region" value="transcribed" />
-      <output name="out_file1" value="cf-gene2exon.dat"/>
+      <output name="out_file1" file="cf-gene2exon.dat"/>
     </test>
   </tests>
 <help>
diff --git a/tools/filters/ucsc_gene_bed_to_intron_bed.xml b/tools/filters/ucsc_gene_bed_to_intron_bed.xml
index 0ead6e8fc70..c544cca9021 100644
--- a/tools/filters/ucsc_gene_bed_to_intron_bed.xml
+++ b/tools/filters/ucsc_gene_bed_to_intron_bed.xml
@@ -11,7 +11,7 @@
   <tests>
     <test>
       <param name="input1" value="3.bed" /> 
-      <output name="out_file1" value="cf-gene2intron.dat"/>
+      <output name="out_file1" file="cf-gene2intron.dat"/>
     </test>
   </tests>
 <help>
diff --git a/tools/stats/gsummary.xml b/tools/stats/gsummary.xml
index 08c8ada934c..cb178d90533 100644
--- a/tools/stats/gsummary.xml
+++ b/tools/stats/gsummary.xml
@@ -15,7 +15,7 @@
     <test>
       <param name="cond" value="c2"/>
       <param name="input" value="1.bed"/>
-      <output name="out_file1" value="sta_summary.dat"/>
+      <output name="out_file1" file="sta_summary.dat"/>
     </test>
   </tests>
   <help>