Update scatterplot.xml to use header names

tools/scatterplot/.shed.yml

@@ -8,4 +8,5 @@ long_description: |
 name: scatterplot
 owner: devteam
 remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot
+homepage_url: https://github.com/galaxyproject/tools-devteam/
 type: unrestricted

tools/scatterplot/scatterplot.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 # Greg Von Kuster
 
+# flake8: noqa
+
 from __future__ import print_function
 
 import sys
@@ -24,41 +26,43 @@ def main():
     in_fname = sys.argv[1]
     out_fname = sys.argv[2]
     try:
-        columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
-    except:
-        stop_err( "Columns not specified, your query does not contain a column of numerical data." )
+        columns = int(sys.argv[3]) - 1, int(sys.argv[4]) - 1
+    except Exception:
+        stop_err(
+            "Columns not specified, your query does not contain a column of numerical data."
+        )
     title = sys.argv[5]
     xlab = sys.argv[6]
     ylab = sys.argv[7]
 
     matrix = []
     skipped_lines = 0
     first_invalid_line = 0
-    invalid_value = ''
+    invalid_value = ""
     invalid_column = 0
     i = 0
-    for i, line in enumerate( open( in_fname ) ):
+    for i, line in enumerate(open(in_fname)):
         valid = True
-        line = line.rstrip( '\r\n' )
-        if line and not line.startswith( '#' ):
+        line = line.rstrip("\r\n")
+        if line and not line.startswith("#"):
             row = []
-            fields = line.split( "\t" )
+            fields = line.split("\t")
             for column in columns:
                 try:
                     val = fields[column]
                     if val.lower() == "na":
-                        row.append( float( "nan" ) )
+                        row.append(float("nan"))
                     else:
-                        row.append( float( fields[column] ) )
-                except:
+                        row.append(float(fields[column]))
+                except Exception:
                     valid = False
                     skipped_lines += 1
                     if not first_invalid_line:
                         first_invalid_line = i + 1
                         try:
                             invalid_value = fields[column]
-                        except:
-                            invalid_value = ''
+                        except Exception:
+                            invalid_value = ""
                         invalid_column = column + 1
                     break
         else:
@@ -68,22 +72,29 @@ def main():
                 first_invalid_line = i + 1
 
         if valid:
-            matrix.append( row )
+            matrix.append(row)
 
     if skipped_lines < i:
         try:
-            a = numpy2ri(array( matrix ))
-            r.pdf( out_fname, 8, 8 )
-            r.plot( a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
+            a = numpy2ri(array(matrix))
+            r.pdf(out_fname, 8, 8)
+            r.plot(a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19)
             r.dev_off()
         except Exception as exc:
-            stop_err( "%s" % str( exc ) )
+            stop_err("%s" % str(exc))
     else:
-        stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
+        stop_err(
+            "All values in both columns %s and %s are non-numeric or empty."
+            % (sys.argv[3], sys.argv[4])
+        )
 
-    print("Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] ))
+    print("Scatter plot on columns %s, %s. " % (sys.argv[3], sys.argv[4]))
     if skipped_lines > 0:
-        print("Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column ))
+        print(
+            "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric."
+            % (skipped_lines, first_invalid_line, invalid_value, invalid_column)
+        )
+
 
 if __name__ == "__main__":
     main()

tools/scatterplot/scatterplot.xml

@@ -1,9 +1,15 @@
-<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.3">
+<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.3+galaxy0">
   <description>of two numeric columns</description>
   <requirements>
     <requirement type="package" version="1.9">numpy</requirement>
     <requirement type="package" version="2.8.5">rpy2</requirement>
+    <requirement type="package" version="3.0">libgfortran</requirement>
   </requirements>
+<!-- 
+  <environment_variables>
+    <environment_variable name="R_HOME">\$(R RHOME)</environment_variable>
+  </environment_variables> -->
+
   <command><![CDATA[
       python '$__tool_directory__/scatterplot.py'
         '$input'
@@ -17,8 +23,21 @@
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
-    <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
-    <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
+    <conditional name="cols">
+        <param name="header" type="select" label="Does the table have a header?" refresh_on_change="true" help="If the table has a header, columns can be selected by name instead of the index.">
+            <option value="yes" selected="true">yes</option>
+            <option value="no">no</option>
+        </param>
+        <when value="yes">
+          <param name="col1" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for x axis" />
+          <param name="col2" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for y axis" />            
+        </when>
+        <when value="no">
+          <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
+          <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
+        </when>
+    </conditional>
+
     <param name="title" type="text" value="Scatterplot" label="Plot title"/>
     <param name="xlab" type="text" value="V1" label="Label for x axis"/>
     <param name="ylab" type="text" value="V2" label="Label for y axis"/>
@@ -76,5 +95,6 @@ This tool creates a simple scatter plot between two variables containing numeric
 ]]>
 </help>
 <citations>
+  <citation type="doi">10.1038/s41586-020-2649-2</citation>
 </citations>
 </tool>