--- a/protein_rna_correlation.xml	Sun Jun 17 05:06:18 2018 -0400
+++ b/protein_rna_correlation.xml	Wed Jun 20 20:43:56 2018 -0400
@@ -1,28 +1,20 @@
-<tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.1">
-  <description>Correlation between protein and rna expression (Single Sample)</description>
+<tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.0.2">
+  <description>Correlation between protein and transcript expression  </description>
   <requirements>
-    <requirement type="package" version="3.3.1">r-base</requirement>
-    <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
-    <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
-    <requirement type="package" version="1.9">rmarkdown</requirement>
-    <requirement type="package" version="1.9">MASS</requirement>
-    <requirement type="package" version="1.8-23">mgcv</requirement>
-    <requirement type="package" version="0.4.1">DMwR</requirement>
-    <requirement type="package" version="1.11.4">data.table</requirement>
-    <requirement type="package" version="3.0.1">gplots</requirement>
-    <requirement type="package" version="0.20-35">lattice</requirement>
-    <requirement type="package" version="3.5.0">grid</requirement>
-    <requirement type="package" version="3.1-137">nlme</requirement>
+    <requirement type="package" version="3.2.1">R</requirement>
+    <requirement type="package" version="0.0.1">r-protrnacorr</requirement>
+    <requirement type="package" version="1.5.0">x11</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>
     </param>
-    <param name="pe_idcol" type="integer">
+    <param name="pe_idcol" type="integer" value="1">
       <label>Column: Protein/Gene ID</label>
     </param>
-    <param name="pe_expcol" type="integer">
+    <param name="pe_expcol" type="integer" value="1">
       <label>Column: Protein Expression Values</label>
     </param>
     
@@ -30,41 +22,41 @@
       <label>Input RNA Expression File</label>
     </param>
     
-    <param name="ge_idcol" type="integer">
+    <param name="ge_idcol" type="integer" value="1">
       <label>Column: RNA/Gene ID</label>
     </param>
-    <param name="ge_expcol" type="integer">
+    <param name="ge_expcol" type="integer" value="1">
       <label>Column: RNA Expression Values</label>
     </param>
     
-    <param name="pe_idtype" type="select">
-        <option value='ensembl' selected>Ensembl</option>
-        <option value='uniprot'>Uniprot</option>
-        <option value='hgnc'>HGNC</option>
+    <param name="pe_idtype" type="select" label="Protein ID type">
+        <option value="Ensembl_with_version" selected="True">Ensembl</option>
+        <option value="uniprot">Uniprot</option>
+        <option value="hgnc">HGNC</option>
     </param>
     
-    <param name="ge_idtype" type="select">
-        <option value='ensembl' selected>Ensembl</option>
-        <option value='uniprot'>Uniprot</option>
-        <option value='hgnc'>HGNC</option>
+    <param name="ge_idtype" type="select" label="Transcript ID type">
+        <option value="Ensembl_with_version" selected="True">Ensembl</option>
+        <option value="uniprot">Uniprot</option>
+        <option value="hgnc">HGNC</option>
     </param>
     
     <param name="organism_map" type="data" format="tabular">
         <label>Biomart ID Mapping file (.map)</label>
     </param>
     
-    <param name="writeMapUnmap" type="boolean">
+    <param name="writeMapUnmap" type="boolean" checked="true" truevalue="1" falsevalue="0">
       <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
     </param>
     
-    <param name="doScale" type="boolean">
+    <param name="doScale" type="boolean" checked="true" truevalue="1" falsevalue="0">
       <label>Scale the abundance values</label>
     </param>
     
   </inputs>
   
   <outputs>
-    <data format="html" name="html_file" label="protein_rna_corr_${tool_name}.html"/>
+    <data format="html" name="html_file" label="protein_rna_corr_${tool.name}.html"/>
   </outputs>
   
   <tests>
@@ -78,14 +70,23 @@
             <param name="pe_idtype" value="Ensembl_with_version"/>
             <param name="ge_idtype" value="Ensembl_with_version"/>
             <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/>
-            <param name="writeMapUnmap" value="1"/>
-            <param name="doScale" value="1"/>
-            <output name="html_file" file="PE_abundance_GE_abundance_pearson.html"/>
+            <param name="writeMapUnmap" value="true"/>
+            <param name="doScale" value="true"/>
+            <output name="html_file" file="protein_rna_corr_protein_transcript_correlation.html"/>
         </test>
   </tests>
     
-  <help>
+  <help><![CDATA[
 Proteome Transcriptome Correlation
 Developer: Priyabrata Panigrahi
-  </help>
+  ]]></help>
+  <citations>
+      <citation type="bibtex">
+@misc{protein_rna_correlation,
+    author={Panigrahi, Priyabrata},
+    year={2018},
+    title={ProteinRNACorrelation}
+}
+      </citation>
+    </citations>
 </tool>