--- a/get_length_and_gc_content.xml	Sun Feb 28 11:52:10 2016 -0500
+++ b/get_length_and_gc_content.xml	Thu Mar 03 09:56:51 2016 -0500
@@ -1,9 +1,10 @@
-<tool id="length_and_gc_content" name="gene length and gc content from gtf file" version="0.1.0">
-    <description />
-    <requirements>
-        <requirement type="package" version="3.2.1">R</requirement>
-        <requirement type="package" version="1.22.0">goseq</requirement>
-    </requirements>
+<tool id="length_and_gc_content" name="gene length and gc content" version="0.1.0">
+    <description>from GTF file</description>
+    <macros>
+        <import>go_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command interpreter="Rscript">
         get_length_and_gc_content.r --gtf "$gtf"
         #if $fastaSource.genomeSource == "indexed":
@@ -11,10 +12,11 @@
         #else:
             --fasta "$fastaSource.fasta_history"
         #end if
-        --output "$output"
+        --length "$length"
+        --gc_content "$gc_content"
     </command>
     <inputs>
-        <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" />
+        <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" format="gtf" />
         <conditional name="fastaSource">
             <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select">
                 <option value="indexed">Use a built-in fasta</option>
@@ -26,19 +28,40 @@
             </param>
         </when>
         <when value="history">
-            <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta_history" type="data" />
+            <param format="fasta" label="Select a fasta file that matches the supplied GTF file" name="fasta_history" type="data" />
         </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" label="length and gc content" name="output" />
+        <data format="tabular" label="gene length" name="length">
+            <!-- future: set this when 16.04 has been released
+            <actions>
+                <action name="column_names" type="metadata" default="gene,length" />
+            </actions>
+            -->
+        </data>
+        <data format="tabular" label="gene gc content" name="gc_content">
+            <!-- future: set this when 16.04 has been released
+             <actions>
+                <action name="column_names" type="metadata" default="gene,gc_content" />
+            </actions>
+            -->
+        </data>
     </outputs>
-    <tests></tests>
+    <tests>
+        <test>
+            <param name="gtf" value="in.gtf" ftype="gtf"></param>
+            <param name="fastaSource|genomeSource" value="history"></param>
+            <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param>
+            <output name="length" file="length.tab"></output>
+            <output name="gc_content" file="gc.tab"></output>
+        </test>
+    </tests>
     <help>
 
         **What it does**
 
-        Returns a tabular file with gene name, length and GC content, based on a supplied GTF and a FASTA file.
+        Returns a tabular file with gene id and length and a tabular file with gene id and GC content, based on a supplied GTF and a FASTA file.
 
 
         </help>