Mercurial > repos > joachim-jacob > blat

diff blat_wrapper.xml @ 1:da4426cac227 draft

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Fixed tests
author Joachim Jacob <joachim.jacob@gmail.com>
date Wed, 24 Jul 2013 16:23:44 +0200
parents 3cec538aab33
children df0c23b49a81
line wrap: on
line diff
--- 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>