From d6d9a6f79eb98d494a2487ebc7c101a934ed483e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 6 Feb 2012 15:43:05 -0600
Subject: [PATCH] Adding plink requirement tag for various rgenetics tools
 requiring plink.

---
 tools/rgenetics/rgCaCo.xml    | 1 +
 tools/rgenetics/rgClean.xml   | 1 +
 tools/rgenetics/rgGLM.xml     | 1 +
 tools/rgenetics/rgLDIndep.xml | 1 +
 tools/rgenetics/rgQC.xml      | 3 ++-
 tools/rgenetics/rgTDT.xml     | 2 ++
 6 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/tools/rgenetics/rgCaCo.xml b/tools/rgenetics/rgCaCo.xml
index 78355f572dc..4a0aac2a784 100644
--- a/tools/rgenetics/rgCaCo.xml
+++ b/tools/rgenetics/rgCaCo.xml
@@ -1,4 +1,5 @@
 <tool id="rgCaCo1" name="Case Control:">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <description>for unrelated subjects</description>
     <command interpreter="python">
         rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title"  '$out_file1' '$logf' '$logf.files_path' '$gffout'
diff --git a/tools/rgenetics/rgClean.xml b/tools/rgenetics/rgClean.xml
index 855c397fd6c..98566157c8a 100644
--- a/tools/rgenetics/rgClean.xml
+++ b/tools/rgenetics/rgClean.xml
@@ -1,4 +1,5 @@
 <tool id="rgClean1" name="Clean genotypes:">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <description>filter markers, subjects</description>
 
     <command interpreter="python">
diff --git a/tools/rgenetics/rgGLM.xml b/tools/rgenetics/rgGLM.xml
index 46931655837..ab72f486d40 100644
--- a/tools/rgenetics/rgGLM.xml
+++ b/tools/rgenetics/rgGLM.xml
@@ -1,4 +1,5 @@
 <tool id="rgGLM1" name="Linear Models:" version="0.2">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <description>for genotype data</description>
     <code file="rgGLM_code.py"/>
     <command interpreter="python">
diff --git a/tools/rgenetics/rgLDIndep.xml b/tools/rgenetics/rgLDIndep.xml
index abf9f225a1d..144edfad544 100644
--- a/tools/rgenetics/rgLDIndep.xml
+++ b/tools/rgenetics/rgLDIndep.xml
@@ -1,4 +1,5 @@
 <tool id="rgLDIndep1" name="LD Independent:">
+    <requirements><requirement type="package">plink</requirement></requirements>
     <code file="rgLDIndep_code.py"/>
 
     <description>filter high LD pairs - decrease redundancy</description>
diff --git a/tools/rgenetics/rgQC.xml b/tools/rgenetics/rgQC.xml
index 4d20c9d2423..19b243db57f 100644
--- a/tools/rgenetics/rgQC.xml
+++ b/tools/rgenetics/rgQC.xml
@@ -1,5 +1,6 @@
 <tool id="rgQC1" name="QC reports:">
-
+    <requirements><requirement type="package">plink</requirement></requirements>
+    
     <description>Marker and Subject measures</description>
 
     <command interpreter="python">
diff --git a/tools/rgenetics/rgTDT.xml b/tools/rgenetics/rgTDT.xml
index 4abb5d83958..18d36c6f5bd 100644
--- a/tools/rgenetics/rgTDT.xml
+++ b/tools/rgenetics/rgTDT.xml
@@ -1,4 +1,6 @@
 <tool id="rgTDT1" name="Transmission Distortion:">
+    <requirements><requirement type="package">plink</requirement></requirements>
+
     <description>for family data</description>
 
     <command interpreter="python">