diff cummerbund_wrapper.xml @ 2:5de9fff7ccf7

fix for warnings on empty conditional inputs

--- a/cummerbund_wrapper.xml	Tue Feb 14 11:58:56 2012 -0500
+++ b/cummerbund_wrapper.xml	Tue Feb 14 13:00:16 2012 -0500
@@ -1,10 +1,13 @@
-<tool id="cummerbund" name="cummeRbund" version="0.0.1">
-    <description>is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
+<tool id="cummerbund" name="cummeRbund" version="0.0.2">
+    
+    <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
+    
     <command interpreter="python">
         cummerbund_wrapper.py
             --r-script ${script_file}
             --html-report-from-directory "${output_html}" "${output_html.files_path}"
     </command>
+    
     <inputs>
         <conditional name="backend_database_source">
             <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?">
@@ -44,12 +47,15 @@
 					<option value="expressionbarplot">Expression Bar Plot</option>
 				</param>
 				<when value="density">
+					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
 				</when>
 				<when value="boxplot">
+					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
 				</when>
 				<when value="scatter">
 					<param name="x" type="text" label="Sample name for x axis"/>
 					<param name="y" type="text" label="Sample name for y axis"/>
+					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
 					<param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/>
 					<conditional name="multiple_genes">
 						<param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
@@ -91,6 +97,9 @@
 						<option value="tss">TSS</option>
 						<option value="cds">CDS</option>
 					</param>
+					<repeat name="genes" title="Genes">
+						<param name="gene_id" type="text" label="Gene ID"/>
+					</repeat>
 					<param name="clustering" type="select" label="Cluster by">
 						<option value="row">Row</option>
 						<option value="column">Column</option>
@@ -99,10 +108,8 @@
 					</param>
 					<param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
 					<param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
+					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
 					<param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/>
-					<repeat name="genes" title="Genes">
-						<param name="gene_id" type="text" label="Gene ID"/>
-					</repeat>
 				</when>
 				<when value="cluster">
 					<param name="features" type="select" label="Expression levels to plot?">
@@ -111,11 +118,11 @@
 						<option value="tss">TSS</option>
 						<option value="cds">CDS</option>
 					</param>
-                    <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/>
-                    <param name="iter_max" type="text" value="100" label="Max iterations"/>
 					<repeat name="genes" title="Genes">
 						<param name="gene_id" type="text" label="Gene ID"/>
 					</repeat>
+                    <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/>
+                    <param name="iter_max" type="text" value="100" label="Max iterations"/>
 				</when>
 				<when value="expressionplot">
 					<param name="features" type="select" label="Expression levels to plot?">
@@ -124,10 +131,11 @@
 						<option value="tss">TSS</option>
 						<option value="cds">CDS</option>
 					</param>
+					<param name="gene_id" type="text" label="Gene ID"/>
+					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
                     <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM
           values for each condition?"/>
                     <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
-					<param name="gene_id" type="text" label="Gene ID"/>
 				</when>
 				<when value="expressionbarplot">
 					<param name="features" type="select" label="Expression levels to plot?">
@@ -136,12 +144,14 @@
 						<option value="tss">TSS</option>
 						<option value="cds">CDS</option>
 					</param>
+					<param name="gene_id" type="text" label="Gene ID"/>
+					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
                     <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
-					<param name="gene_id" type="text" label="Gene ID"/>
 				</when>
 			</conditional>
 		</repeat>
     </inputs>
+    
     <outputs>
         <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
             <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>