--- a/snpSift_caseControl.xml	Thu Nov 28 08:16:11 2013 -0600
+++ b/snpSift_caseControl.xml	Fri Nov 29 09:27:22 2013 -0500
@@ -1,13 +1,13 @@
 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.4">
-  <description>Count samples are in 'case' and 'control' groups.</description>
-  <!-- 
-    You will need to change the path to wherever your installation is.
-    You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
-  -->
-  <requirements>
-                <requirement type="package" version="3.4">snpEff</requirement>
-  </requirements>
-  <command>
+    <description>Count samples are in 'case' and 'control' groups.</description>
+    <!-- 
+        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
+    -->
+    <expand macro="requirements" />
+    <macros>
+        <import>snpEff_macros.xml</import>
+    </macros>
+    <command>
     java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
     #if $name.__str__.strip() != '':
       -name $name
@@ -18,79 +18,73 @@
       -tfam "$ctrl.tfam"
     #end if
     $input > $output
-  </command>
-  <inputs>
-    <param format="vcf" name="input" type="data" label="VCF input"/>
-    <conditional name="ctrl">
-      <param name="ctrl_src" type="select" label="Case Control defined in">
-        <option value="caseString">Case Control String</option>
-        <option value="tfam">TFAM</option>
-      </param>
-      <when value="caseString">
-        <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
-          <help>
-             Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
-          </help>
-          <validator type="regex" message="must be  only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
+    </command>
+    <inputs>
+        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
+        <conditional name="ctrl">
+            <param name="ctrl_src" type="select" label="Case Control defined in">
+            <option value="caseString">Case Control String</option>
+            <option value="tfam">TFAM file</option>
         </param>
-      </when>
-      <when value="tfam">
-        <param format="tabular" name="tfam" type="data" label="PLINK TFAM file"/>
-      </when>
-    </conditional>
-    <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags">
-        <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="output" />
-  </outputs>
-        <stdio>
-          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-          <exit_code range="1:"  level="fatal"   description="Error" />
-        </stdio>
-        <tests>
+        <when value="caseString">
+            <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
+            <help>
+                Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
+            </help>
+            <validator type="regex" message="must be  only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
+            </param>
+        </when>
+        <when value="tfam">
+            <param format="tabular" name="tfam" type="data" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/>
+        </when>
+        </conditional>
+        <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags">
+            <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="output" />
+    </outputs>
+    <expand macro="stdio" />
+    <tests>
+        <test>
+            <param name="input" ftype="vcf" value="test.private.01.vcf"/>
+            <param name="ctrl_src" value="caseString"/>
+            <param name="caseControlStr" value="--"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Cases=0,0,0;" />
+                    <has_text text="Controls=0,0,0;" />
+                </assert_contents>
+            </output>
+        </test>
 
-            <test>
-                <param name="input" ftype="vcf" value="test.private.01.vcf"/>
-                <param name="ctrl_src" value="caseString"/>
-                <param name="caseControlStr" value="--"/>
-                <output name="output">
-                    <assert_contents>
-                        <has_text text="Cases=0,0,0;" />
-                        <has_text text="Controls=0,0,0;" />
-                    </assert_contents>
-                </output>
-            </test>
+        <test>
+            <param name="input" ftype="vcf" value="test.private.02.vcf"/>
+            <param name="ctrl_src" value="caseString"/>
+            <param name="caseControlStr" value="--"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Cases=0,0,0;" />
+                    <has_text text="Controls=2,0,4;" />
+                </assert_contents>
+            </output>
+        </test>
 
-            <test>
-                <param name="input" ftype="vcf" value="test.private.02.vcf"/>
-                <param name="ctrl_src" value="caseString"/>
-                <param name="caseControlStr" value="--"/>
-                <output name="output">
-                    <assert_contents>
-                        <has_text text="Cases=0,0,0;" />
-                        <has_text text="Controls=2,0,4;" />
-                    </assert_contents>
-                </output>
-            </test>
-
-            <test>
-                <param name="input" ftype="vcf" value="test.private.02.vcf"/>
-                <param name="name" value=""/>
-                <param name="ctrl_src" value="caseString"/>
-                <param name="caseControlStr" value="-+"/>
-                <output name="output">
-                    <assert_contents>
-                        <has_text text="Cases=1,0,2;" />
-                        <has_text text="Controls=1,0,2;" />
-                    </assert_contents>
-                </output>
-            </test>
-
-        </tests>
-
-  <help>
+        <test>
+            <param name="input" ftype="vcf" value="test.private.02.vcf"/>
+            <param name="name" value=""/>
+            <param name="ctrl_src" value="caseString"/>
+            <param name="caseControlStr" value="-+"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Cases=1,0,2;" />
+                    <has_text text="Controls=1,0,2;" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
 
 **SnpSift CaseControl**
 
@@ -119,15 +113,9 @@
   - Case / Control column designation = ""++++------"
 
 
-For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
-
-SnpEff citation:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+@EXTERNAL_DOCUMENTATION@
 
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
-
-
+@CITATION_SECTION@
 
   </help>
 </tool>