--- a/metaquantome_viz.xml	Tue Nov 24 15:08:30 2020 +0000
+++ b/metaquantome_viz.xml	Sat Jan 30 17:57:10 2021 +0000
@@ -117,7 +117,7 @@
             #if $mode_args.plot.heatmap.filter_to_sig:
               --filter_to_sig
               --alpha=$mode_args.plot.heatmap.alpha
-              --fc_corr_p='mode_args.plot.fc_corr_p'
+              --fc_corr_p='$mode_args.plot.heatmap.fc_corr_p'
             #end if
             #if $mode_args.plot.feature_cluster_size:
                 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
@@ -165,16 +165,11 @@
               the easiest fix is to increase the plot dimensions
             </p>
           </body>
-        </html>" > wrapped_outfile.html
-    && >&2 ls
-    #if $mode_args.plot.plottype in ["heatmap"]
-        && mv 'feature_cluster_${safename}.txt' '$heatmap_feature_cluster'
-        && mv 'sample_cluster_${safename}.txt' '$heatmap_sample_cluster'
-    #end if
-    #if $mode_args.plot.plottype in ["pca"]
-        && mv 'PC_data_${safename}.txt' '$pca_sample_cluster'
-    #end if
-      
+        </html>" > wrapped_outfile.html &&
+        if test -f 'feature_cluster_${infile.name}.txt'; then mv 'feature_cluster_${infile.name}.txt' feature_cluster_data.txt; fi && 
+        if test -f 'sample_cluster_${infile.name}.txt'; then mv 'sample_cluster_${infile.name}.txt' sample_cluster_data.txt; fi &&
+        if test -f 'PC_Data_${infile.name}.txt'; then mv 'PC_Data_${infile.name}.txt' PC_Data.txt; fi
+
     ]]></command>
     <inputs>
       <param argument="--infile" type="data"
@@ -346,16 +341,19 @@
       </data>
       
       <data format="tabular" name="heatmap_feature_cluster"
-        label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} feature cluster data">
+        label="${mode_args.plot.plottype}: feature cluster data"
+        from_work_dir="feature_cluster_data.txt">
         <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
       </data>
       <data format="tabular" name="heatmap_sample_cluster"
-        label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
+        label="${mode_args.plot.plottype}: sample cluster data"
+        from_work_dir="sample_cluster_data.txt">
         <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
       </data>
       
       <data format="tabular" name="pca_sample_cluster"
-        label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
+        label="${mode_args.plot.plottype}: sample cluster data"
+        from_work_dir="PC_Data.txt">
         <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
       </data>
       
@@ -390,14 +388,24 @@
             </output>
         </test>
         <test expect_num_outputs="3">
-             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
-             <param name="mode" value="t" />
-             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-             <param name="plottype" value="heatmap" />
-             <output name="wrapped_outfile">
-                <assert_contents>
-                    <has_text text="To download the image" />
-                </assert_contents>
+            <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
+            <param name="mode" value="t" />
+            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+            <param name="plottype" value="heatmap" />
+            <param name="filter_to_sig" />
+            <param name="alpha" value="0.05" />
+            <param name="fc_corr_p" value="corrected_p_NS_over_WS" />
+            <param name="feature_cluster_size" value="2" />
+            <param name="sample_cluster_size" value="2" />
+            <output name="wrapped_outfile">
+              <assert_contents>
+                  <has_text text="To download the image" />
+              </assert_contents>
+            </output>
+            <output name="heatmap_feature_cluster">
+              <assert_contents>
+                  <has_text text="481" />
+              </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="2">
@@ -409,7 +417,7 @@
                 <assert_contents>
                     <has_text text="To download the image" />
                 </assert_contents>
-            </output>
+              </output>
         </test>
         <test expect_num_outputs="2">
              <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>