--- a/cuffdiff_wrapper.xml	Fri Dec 19 11:57:43 2014 -0500
+++ b/cuffdiff_wrapper.xml	Tue Dec 23 15:55:31 2014 -0500
@@ -1,12 +1,16 @@
-<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.0">
+<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.1">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
-    <expand macro="requirements" />
+    <requirements>
+        <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
+        <requirement type="package" version="2.2.1">cufflinks</requirement>
+        <requirement type="package" version="2.8.2">cummeRbund</requirement>
+    </requirements>
     <expand macro="stdio" />
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
-    <command>
+    <command><![CDATA[
         cuffdiff
             --no-update-check
             --FDR=$fdr
@@ -64,6 +68,9 @@
             $gtf_input
 
             @CONDITION_SAMPLES@
+            &&
+            R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}"
+            ]]>
     </command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
@@ -179,52 +186,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <!-- Optional read group datasets. -->
-        <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <!-- Standard datasets. -->
-        <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" />
-        <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" />
-        <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" />
-        <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" />
-        <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
-        <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
-
-        <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" />
-        <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
-        <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
-
-        <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" />
-        <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
-        <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
-
-        <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" />
-        <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
-        <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
+        <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" />
     </outputs>
 
     <tests>
@@ -254,17 +216,7 @@
                 <param name="do_normalization" value="No" />
                 <param name="multiread_correct" value="No"/>
                 <param name="sAdditional" value="No"/>
-                <output name="splicing_diff" file="cuffdiff_out9.txt"/>
-                <output name="promoters_diff" file="cuffdiff_out10.txt"/>
-                <output name="cds_diff" file="cuffdiff_out11.txt"/>
-                <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
-                <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
-                <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
-                <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
-                <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
-                <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
-                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
-                <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
+                <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/>
         </test>
     </tests>
     <help>