# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1408670548 14400
# Node ID 7112ee9a7ada33e0725ab76a9af6565b1a0b7840

first

diff -r 000000000000 -r 7112ee9a7ada test_dependency.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_dependency.sh	Thu Aug 21 21:22:28 2014 -0400
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+results=$1 #X-linked candidates written here
+
+fake_input1=${2}
+fake_input2=${3}
+
+echo "LINKYX_PATH: " $LINKYX_PATH
+
+cat ${LINKYX_PATH}/demo_files/reference.fasta >>$results
+
+
+
diff -r 000000000000 -r 7112ee9a7ada test_dependency.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_dependency.xml	Thu Aug 21 21:22:28 2014 -0400
@@ -0,0 +1,22 @@
+<tool id="test_dependency" name="test_dependency">
+      <description>Test toolshed dependency</description>
+      <command interpreter="bash">test_dependency.sh $output $input1 $input2</command>
+      <inputs>
+        <param format="fastq" name="input1" type="data" label="Fake left reads"/>
+        <param format="fastq" name="input2" type="data" label="Fake right reads"/>
+      </inputs>
+      <outputs>
+        <data format="fasta" name="output" />
+      </outputs>
+  
+     <tests>
+       <test>
+        <output name="out_file1" file="Y_results.txt"/>
+       </test>
+     </tests>
+   
+     <help>
+   Test dependency
+     </help>
+   
+   </tool>
\ No newline at end of file
diff -r 000000000000 -r 7112ee9a7ada tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Aug 21 21:22:28 2014 -0400
@@ -0,0 +1,5 @@
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+</tool_dependency>