diff samples_qccheck.xml @ 8:258c64019e50 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 811337eaab815f54f0fd93a3dd23a1153993ea2a

--- a/samples_qccheck.xml	Mon Jun 20 11:44:50 2016 -0400
+++ b/samples_qccheck.xml	Tue Jun 28 12:22:40 2016 -0400
@@ -9,41 +9,41 @@
         <exit_code range="1:"/>
     </stdio>
     <command><![CDATA[
-        
+
         ln -s "${matrix}" "input.matrix"
-        
+
         &&
-        
+
         PtR
         --matrix "input.matrix"
-        
+
         --samples "${samples}"
-        
+
         --CPM --log2 --compare_replicates
-        
+
         &&
-        
+
         PtR
         --matrix "input.matrix"
-        
+
         --samples "${samples}"
-        
+
         --CPM --log2 --sample_cor_matrix
-        
+
         &&
-        
+
         PtR
         --matrix "input.matrix"
-        
+
         --samples "${samples}"
-        
+
         --CPM --log2 --prin_comp 3
-        
+
         && mkdir out_pdf
         && mv *rep_compare.pdf out_pdf/
         && mv *sample_cor_matrix.pdf out_pdf/
         && mv *principal_components.pdf out_pdf/
-        
+
     ]]></command>
     <inputs>
         <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
@@ -51,7 +51,7 @@
     </inputs>
     <outputs>
         <collection name="reports" type="list" label="Quality check result files on ${on_string}">
-            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" />
+            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
         </collection>
     </outputs>
     <tests>
@@ -106,7 +106,7 @@
 .. _Trinity: http://trinityrnaseq.github.io
 ]]>
     </help>
-    
+
      <citations>
         <citation type="doi">10.1038/nbt.1883</citation>
     </citations>