diff protein_rna_correlation.xml @ 0:fc89f8c3b777 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_rna_correlation.xml	Sun Jun 17 04:20:06 2018 -0400
@@ -0,0 +1,96 @@
+<tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.0">
+  <description>Correlation between protein and rna expression (Single Sample)</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>
+  </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" "$html_file.files_path"]]></command>
+  
+  <inputs>
+    <param name="pe_exp" type="data" format="tabular">
+      <label>Input Protein Expression File</label>
+    </param>
+    <param name="pe_idcol" type="integer">
+      <label>Column: Protein/Gene ID</label>
+    </param>
+    <param name="pe_expcol" type="integer">
+      <label>Column: Protein Expression Values</label>
+    </param>
+    
+    <param name="ge_exp" type="data" format="tabular">
+      <label>Input RNA Expression File</label>
+    </param>
+    
+    <param name="ge_idcol" type="integer">
+      <label>Column: RNA/Gene ID</label>
+    </param>
+    <param name="ge_expcol" type="integer">
+      <label>Column: RNA Expression Values</label>
+    </param>
+    
+    <param name="pe_idtype" type="select">
+        <option value='ensembl' selected>Ensembl</option>
+        <option value='uniprot'>Uniprot</option>
+        <option value='hgnc'>HGNC</option>
+    </param>
+    
+    <param name="ge_idtype" type="select">
+        <option value='ensembl' selected>Ensembl</option>
+        <option value='uniprot'>Uniprot</option>
+        <option value='hgnc'>HGNC</option>
+    </param>
+    
+    <param name="organism_map" type="data" format="tabular">
+        <label>Biomart ID Mapping file (.map)</label>
+    </param>
+    
+    <!--<param name="method" type="select" label="Correlation Method">
+    <option value="pearson" selected="true">Pearson</option>
+    <option value="spearman">Spearman</option>
+    <option value="kendall">Kendall</option>
+    </param>-->
+    
+    <param name="writeMapUnmap" type="boolean">
+      <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
+    </param>
+    
+    <param name="doScale" type="boolean">
+      <label>Scale the abundance values</label>
+    </param>
+    
+  </inputs>
+  
+  <outputs>
+    <data format="html" name="html_file" label="protein_rna_corr_${tool_name}.html"/>
+  </outputs>
+  
+  <tests>
+        <test>
+            <param name="pe_exp" value="PE_mouse_singlesample.txt"/>
+            <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"/>
+            <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"/>
+        </test>
+  </tests>
+    
+  <help>
+Proteome Transcriptome Correlation
+Developer: Priyabrata Panigrahi
+  </help>
+</tool>