# HG changeset patch
# User Joachim Jacob <joachim.jacob@gmail.com>
# Date 1374675824 -7200
# Node ID da4426cac2272a50c2f8c228272262b6d5a1fa75
# Parent  3cec538aab331e9bdca599586ffbb716ae1d11d1
Fixed tests

diff -r 3cec538aab33 -r da4426cac227 blat_wrapper.pl
--- a/blat_wrapper.pl	Thu May 30 07:13:55 2013 -0400
+++ b/blat_wrapper.pl	Wed Jul 24 16:23:44 2013 +0200
@@ -28,16 +28,14 @@
 ########################################################################
 my ($configfile) = @ARGV;
 my (%para);
-open(CONFIG,"<$configfile");
+open(CONFIG,"<",$configfile);
 while (<CONFIG>) {
 	if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; }
 }
 close(CONFIG);
 
 =Excerpt Config parameters
-			## first we pass some galaxy environment variables
-			galtemp==${__new_file_path__}
-			
+
 			## first we pass some galaxy environment variables
 			galtemp==${__new_file_path__}
 			
@@ -76,7 +74,6 @@
 	INFO "$para\tset to\t$para{$para}";
 }
 
-
 # ---------------------- Prepping temp dir ----------------------------#
 ########################################################################
 # within the temporary directory of Galaxy, we create a temporary dir
@@ -90,10 +87,14 @@
 mkdir "$tempdir", 077 unless -d "$tempdir";
 INFO "\nTemporary directory:\n$tempdir";
 
+# --------------------- Checking executable ---------------------------#
+########################################################################
+#~ my $command = "which blat ";
+#~ run_process($command, "Testing path", $tempdir);
 
 # -------------------- Assembling command  ----------------------------#                                                             
 ########################################################################                                                             
-my $command = "blat ";   # this will ultimately be executed
+my $command = "blat ";   			# this will ultimately be executed
 $command .= " $para{'referencepath'}";     
 if ( $para{'range'} ) { 
 	## format checking of the provided range
@@ -118,7 +119,7 @@
 
 if ( $para{'advanced_params.use'} eq "yes" ){
 	delete($para{'advanced_params.use'});
-	$command .= " 	-minScore=$para{'minScore'} -maxGap=$para{'maxGap'} -mask=$para{'mask'} -qMask=$para{'qMask'} -oneOff=$para{'oneOff'}  -minMatch=$para{'minMatch'} -tileSize=$para{'tileSize'} 	-stepSize=$para{'stepSize'} -maxIntron=$para{'maxIntron'} ";
+	$command .= " -minScore=$para{'minScore'} -maxGap=$para{'maxGap'} -mask=$para{'mask'} -qMask=$para{'qMask'} -oneOff=$para{'oneOff'}  -minMatch=$para{'minMatch'} -tileSize=$para{'tileSize'} -stepSize=$para{'stepSize'} -maxIntron=$para{'maxIntron'} ";
 	if($para{'repeats'} eq 'yes' ){
 		$command .= " -repeats=$para{'qMask'}";
 	}
diff -r 3cec538aab33 -r da4426cac227 blat_wrapper.xml
--- a/blat_wrapper.xml	Thu May 30 07:13:55 2013 -0400
+++ b/blat_wrapper.xml	Wed Jul 24 16:23:44 2013 +0200
@@ -1,20 +1,19 @@
-<tool id="blat" name="Align sequences with BLAT" version="1.0.0">
+
+<tool id="blat" name="Align sequences with BLAT" version="1.0.1">
     <!-- Additional info: wrapper compatible with versions ..... -->
     <description>
 		to a reference genome
     </description>
     
-    <version_command/>
+    <version_command>
+    </version_command>
     
     <requirements>
         <requirement type="package" version="1.0.0">blat</requirement>
     </requirements>
     
     <command interpreter="perl">
-        ## it is recommended that you write a wrapper for your tool
-        ## and pass all parameters to that tool, which parses them.
         blat_wrapper.pl $configfile
-
     </command> 
    
     <inputs>
@@ -42,7 +41,7 @@
             </param>
           </when>
           <when value="history">
-            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the sequence database" />
+            <param name="ownFile" type="data" format="fasta" metadata_nameloc="dbkey" label="Select the sequence database" />
           </when>  <!-- history -->
         </conditional>  <!-- refGenomeSource -->
       
@@ -136,30 +135,31 @@
 		</configfile>
 	</configfiles> 
 
-	<tests>
+    <tests>
 		<test>
-          <param name="input" value="input83.fas" />
-          <param name="refGenomeSource.genomeSource" value="history" />
-          <param name="refGenomeSource.ownFile" value="databasetest1.txt" />
-          <param name="q" value="dna" />
-          <param name="t" value="dna" />
-          <param name="advanced_params.use" value="yes" />
-          <param name="advanced_params.tileSize" value="11" />
-          <param name="advanced_params.stepSize" value="11" />
-          <param name="advanced_params.oneOff" value="0" />
-          <param name="advanced_params.minMatch" value="2" />
-          <param name="advanced_params.minScore" value="30" />
-          <param name="advanced_params.maxGap" value="2" />
-          <param name="advanced_params.mask" value="lower" />
-          <param name="advanced_params.qMask" value="lower" />
-          <param name="advanced_params.repeats" value="no" />
-          <param name="advanced_params.trimT" value="no" />
-          <param name="advanced_params.noTrimA" value="yes" />
-          <param name="advanced_params.fine" value="no" />
-          <param name="advanced_params.maxIntron" value="750000" />
-          <param name="advanced_params.extendThroughN" value="no" />
-          <output name="output" file="outputtest1.txt" lines_diff="2"/>     
-        </test>
+			<param name="input" value="input83.fas" ftype="fasta" />
+			<param name="q" value="dna" />
+			<param name="genomeSource" value="history" />
+			<param name="ownFile" value="blatdatabase1.fas" />
+			<param name="t" value="dna" />
+			<param name="use" value="yes" />
+			<param name="tileSize" value="11" />
+			<param name="stepSize" value="11" />
+			<param name="oneOff" value="0" />
+			<param name="tileSize" value="11" />
+			<param name="minMatch" value="2" />
+			<param name="minScore" value="30" />
+			<param name="maxGap" value="2" />
+			<param name="mask" value="lower" />
+			<param name="qMask" value="lower" />
+			<param name="repeats" value="no" />
+			<param name="trimT" value="yes" />
+			<param name="noTrimA" value="no" />
+			<param name="fine" value="no" />
+			<param name="maxIntron" value="750000" />
+			<param name="extendThroughN" value="no" />
+			<output name="output" file="blatoutput1.txt" ftype="tabular" lines_diff="2"/>	
+		</test>
     </tests>
 
     <help>