--- a/cuffmerge_wrapper.xml	Mon Jan 20 11:09:02 2014 -0500
+++ b/cuffmerge_wrapper.xml	Fri Dec 19 11:59:06 2014 -0500
@@ -1,12 +1,12 @@
-<tool id="cuffmerge" name="Cuffmerge" version="0.0.6">
-    <!-- Wrapper supports Cuffmerge versions 1.3 and newer -->
+<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
     <description>merge together several Cufflinks assemblies</description>
-    <requirements>
-        <requirement type="package" version="2.1.1">cufflinks</requirement>
-    </requirements>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <macros>
+      <import>cuff_macros.xml</import>
+    </macros>
     <command interpreter="python">
         cuffmerge_wrapper.py
-        
             --num-threads="\${GALAXY_SLOTS:-4}"
             
             ## Use annotation reference?
@@ -16,29 +16,23 @@
             
             ## Use sequence data?
             #if $seq_data.use_seq_data == "Yes":
-	            -s
+                -s
                 #if $seq_data.seq_source.index_source == "history":
                     --ref_file="${seq_data.seq_source.ref_file}"
                 #else:
                     --index="${seq_data.seq_source.index.fields.path}"
                 #end if
             #end if
-            
+
+            --min-isoform-fraction="${min_isoform_fraction}"
+
             ## Outputs.
             --merged-transcripts="${merged_transcripts}"
-                        
-            ## Inputs.
-            "${first_input}"
-            #for $input_file in $input_files:
-                "${input_file.additional_input}"
-            #end for
-            
+
+            @CUFFLINKS_GTF_INPUTS@
     </command>
     <inputs>
-        <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/>
-        <repeat name="input_files" title="Additional GTF Input Files">
-            <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/>
-        </repeat>
+        <expand macro="cufflinks_gtf_inputs" />
         <conditional name="annotation">
             <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
                 <option value="No">No</option>
@@ -65,7 +59,7 @@
                   <when value="cached">
                     <param name="index" type="select" label="Using reference genome">
                       <options from_data_table="fasta_indexes">
-                        <filter type="data_meta" ref="first_input" key="dbkey" column="1" />
+                        <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
                         <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
                       </options>
                     </param>
@@ -76,6 +70,7 @@
                 </conditional>
             </when>
         </conditional>
+        <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" />
     </inputs>
 
     <outputs>
@@ -87,12 +82,12 @@
             cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf
         -->
         <test>
-            <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/>
-            <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/>
+            <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/>
             <param name="use_ref_annotation" value="Yes"/>
             <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/>
+            <param name="min_isoform_fraction" value="0.08" />
             <param name="use_seq_data" value="No"/>
-			<!-- oId assignment differ/are non-deterministic -->
+            <!-- oId assignment differ/are non-deterministic -->
             <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/>
         </test>
     </tests>
@@ -102,8 +97,8 @@
 
 Cuffmerge is part of Cufflinks_. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
 
-.. _Cufflinks: http://cufflinks.cbcb.umd.edu/
-        
+.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
+
 ------
 
 **Know what you are doing**
@@ -112,7 +107,7 @@
 
 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
 
-.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge
+.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
 
 ------
 
@@ -130,5 +125,9 @@
 
 Merged transcripts file:
 
-Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.    </help>
+Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+    </citations>
 </tool>