# HG changeset patch
# User greg
# Date 1470928515 14400
# Node ID f622abc513d631e000bffee3160e051eb65f5c71
# Parent  5cc7d287decd489116bb75050d3d8e1c8e7c4528
Uploaded

diff -r 5cc7d287decd -r f622abc513d6 bmsb.xml
--- a/bmsb.xml	Thu Aug 11 11:14:27 2016 -0400
+++ b/bmsb.xml	Thu Aug 11 11:15:15 2016 -0400
@@ -2,19 +2,42 @@
 <tool id="bmsb" name="BMSB" version="1.0.0">
     <description></description>
     <requirements>
-        <requirement type="package" version="1.0">bmsb</requirement>
+        <requirement type="package" version="1.3.0">r-optparse</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="0.9.19">r-jsonlite</requirement>
     </requirements>
     <command>
         <![CDATA[
             #import json
             Rscript $__tool_directory__/bmsb.R
             -o "$output"
+            #if str($output_r_logging_cond.output_r_logging) == "yes":
+                -s "true"
+                -m "$output_r_log"
+            #end if
+            #if str($output_r_logging_cond.output_r_logging) == "yes":
+                -e "true"
+                -x "$output_ex_report"
+            #end if
         ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="csv" label="CSV input" />
+        <conditional name="output_r_logging_cond">
+            <param name="output_r_logging" type="select" label="Output R logging?" help="Generate an additional dataset consisting of R messages.">
+                <option value="yes" selected="True">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="no"/>
+            <when value="yes"/>
+        </conditional>
     </inputs>
     <outputs>
+        <data name="output_r_log" format="txt" label="${tool.name} on ${on_string}: R log">
+            <filter>output_r_logging_cond['output_r_logging'] == "yes"</filter>
+        </data>
+        <data name="output_ex_report" format="json" label="${tool.name} on ${on_string}: Experiment report">
+            <filter>output_experiment_report_cond['output_experiment_report'] == "yes"</filter>
+        </data>
         <data name="output" format="RData"/>
     </outputs>
     <help>