--- a/protein_rna_correlation.xml	Sun Jun 17 04:44:29 2018 -0400
+++ b/protein_rna_correlation.xml	Sun Jun 17 04:59:40 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.0">
+<tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.1">
   <description>Correlation between protein and rna expression (Single Sample)</description>
   <requirements>
     <requirement type="package" version="3.3.1">r-base</requirement>
@@ -15,7 +15,6 @@
     <requirement type="package" version="3.1-137">nlme</requirement>
   </requirements>
   <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[protein_rna_correlation.r $pe_exp $ge_exp $pe_idcol $ge_idcol $pe_expcol $ge_expcol $pe_idtype $ge_idtype $organism_map $writeMapUnmap $doScale "$html_file" "$html_file.files_path"]]></command>
-  
   <inputs>
     <param name="pe_exp" type="data" format="tabular">
       <label>Input Protein Expression File</label>
@@ -54,12 +53,6 @@
         <label>Biomart ID Mapping file (.map)</label>
     </param>
     
-    <!--<param name="method" type="select" label="Correlation Method">
-    <option value="pearson" selected="true">Pearson</option>
-    <option value="spearman">Spearman</option>
-    <option value="kendall">Kendall</option>
-    </param>-->
-    
     <param name="writeMapUnmap" type="boolean">
       <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
     </param>
@@ -80,7 +73,6 @@
             <param name="pe_idcol" value="7"/>
             <param name="ge_exp" value="GE_mouse_singlesample.txt"/>
             <param name="ge_idcol" value="1"/>
-            <param name="method" value="pearson"/>
             <param name="pe_expcol" value="13"/>
             <param name="ge_expcol" value="10"/>
             <param name="pe_idtype" value="Ensembl_with_version"/>