# HG changeset patch
# User nilesh
# Date 1373908361 18000
# Node ID c6a790326d1eda4158bd6e585116631a532b60a8
# Parent  4f6349319c0a408fc0f87d74c3faade4f06413dc
moved from test

diff -r 4f6349319c0a -r c6a790326d1e sickle.xml
--- a/sickle.xml	Fri Jul 12 14:01:18 2013 -0500
+++ b/sickle.xml	Mon Jul 15 12:12:41 2013 -0500
@@ -1,7 +1,6 @@
 <tool id="sickle" name="Sickle">
 	<description>Windowed Adaptive Trimming of FastQ data</description>
 	<requirements>
-		<requirement type="package" version="1.2.8">zlib</requirement>
 		<requirement type="package" version="1.21.0">sickle</requirement>
 	</requirements>
 	<command>
@@ -84,7 +83,20 @@
 		<filter>(readtype['single_or_paired'] == 'pe')</filter>
 		</data>
 	</outputs>
-
+	<tests>
+		<param name="single_or_paired" value="pe"/>
+		<param name="input_paired1" value="test.f.fastq"/>
+		<param name="input_paired2" value="test.r.fastq"/>
+		<param name="qual_type" value="illumina"/>
+		<param name="qual_threshold" value="20"/>
+		<param name="length_threshold" value="20"/>
+		<param name="no_five_prime" value="false"/>
+		<param name="discard_n" value="false"/>
+		<output name="output_paired1" value="output.f.fastq"/>
+		<output name="output_paired2" value="output.r.fastq"/>
+		<output name="output_paired_single" value="output.fastq"/>
+	</tests>
+	
 	<help>
 Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses.
 
diff -r 4f6349319c0a -r c6a790326d1e tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jul 12 14:01:18 2013 -0500
+++ b/tool_dependencies.xml	Mon Jul 15 12:12:41 2013 -0500
@@ -1,31 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="zlib" version="1.2.8">
+    <package name="sickle" version="1.21.0">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action>
                 <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action>
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action>
-                <action type="set_environment">
-                    <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/zlib/lib</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        	zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms.
-        </readme>
-    </package>
-    <package name="sickle" version="1.21.0">
-        <install version="1.0">
-            <actions>
                 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action>
-                <action type="shell_command">make LIBS="-L$ENV[ZLIB_PATH] -lz"</action>
+                <action type="shell_command">cd ./sickle &amp;&amp; make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action>
                 <action type="move_file">
-                    <source>sickle</source>
+                    <source>sickle/sickle</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
                 <action type="set_environment">