diff fastq-mcf.xml @ 1:b61f1466ce8f default tip

Add tool_dependencies.xml and test case

--- a/fastq-mcf.xml	Tue Mar 13 14:44:46 2012 -0400
+++ b/fastq-mcf.xml	Mon Apr 01 10:28:17 2013 -0500
@@ -1,7 +1,7 @@
 <tool id="fastq_mcf" name="FastqMcf" version="1.0">
   <description>sequence quality filtering and clipping</description>
   <requirements>
-    <requirement type="binary">fastq-mcf</requirement>
+    <requirement type="package" version="1.1.2-484">ea-utils</requirement>
   </requirements>
   <version_string>fastq-mcf -V</version_string>
   <command>fastq-mcf 
@@ -41,7 +41,9 @@
       #if len($trimming.sampcnt.__str__) > 0
         -s $trimming.sampcnt
       #end if
-      $trimming.ilv3
+      #if len($trimming.ilv3.__str__.strip()) > 0
+        -$trimming.ilv3
+      #end if
       $trimming.rmns
     #end if
     #if $noclip == True :
@@ -120,9 +122,9 @@
         </param>
         <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/>
         <param name="ilv3" type="select" label="illumina PF filtering">
-           <option value=" ">Default</option>
-           <option value="-U">Disable illumina PF filtering</option>
-           <option value="-u">Enable illumina PF filtering</option>
+           <option value="">Default</option>
+           <option value="U">Disable illumina PF filtering</option>
+           <option value="u">Enable illumina PF filtering</option>
         </param>
       </when>
     </conditional>
@@ -143,7 +145,24 @@
       <filter>(noclip == False and mates != None)</filter>
     </data>
   </outputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal"   description="Error" />
+  </stdio>
   <tests>
+    <test>
+      <param name="adpaters" ftype="fasta" value="adapters.fa" />
+      <param name="reads" ftype="fastqillumina" value="test_mcf_reads.fq" />
+      <param name="mates" ftype="fastqillumina" value="test_mcf_mates.fq" />
+      <param name="choice" value="user_set" />
+      <param name="nkeep" value="16" />
+      <param name="qthr" value="15" />
+      <param name="qwin" value="5" />
+      <param name="pctns" value="10" />
+      <param name="ilv3" value="u" />
+      <param name="phred" value="33" />
+      <output name="reads_out" file="testout_mcf_reads.fq" />
+      <output name="mates_out" file="testout_mcf_mates.fq" />
+    </test>
   </tests>
   <help>
 **What it does**
@@ -156,6 +175,8 @@
   Detect N's, and remove from ends
   Remove reads with CASAVA 'Y' flag (purity filtering)
   Discard sequences that are too short after all of the above
+
+
   Keep multiple mate-reads in sync while doing all of the above
 
 .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf