# HG changeset patch
# User devteam
# Date 1406562982 14400
# Node ID c12b0759203b682e4c6c8b5a675d3ee1bd6ed5c2

Imported from capsule None

diff -r 000000000000 -r c12b0759203b scatterplot.png
Binary file scatterplot.png has changed
diff -r 000000000000 -r c12b0759203b scatterplot.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scatterplot.py	Mon Jul 28 11:56:22 2014 -0400
@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+#Greg Von Kuster
+
+import sys
+from rpy import *
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+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." )
+    title = sys.argv[5]
+    xlab = sys.argv[6]
+    ylab = sys.argv[7]
+
+    matrix = []
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_value = ''
+    invalid_column = 0
+    i = 0
+    for i, line in enumerate( file( in_fname ) ):
+        valid = True
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ): 
+            row = []
+            fields = line.split( "\t" )
+            for column in columns:
+                try:
+                    val = fields[column]
+                    if val.lower() == "na": 
+                        row.append( float( "nan" ) )
+                    else:
+                        row.append( float( fields[column] ) )
+                except:
+                    valid = False
+                    skipped_lines += 1
+                    if not first_invalid_line:
+                        first_invalid_line = i + 1
+                        try:
+                            invalid_value = fields[column]
+                        except:
+                            invalid_value = ''
+                        invalid_column = column + 1
+                    break
+        else:
+            valid = False
+            skipped_lines += 1
+            if not first_invalid_line:
+                first_invalid_line = i+1
+
+        if valid:
+            matrix.append( row )
+
+    if skipped_lines < i:
+        try:
+            r.pdf( out_fname, 8, 8 )
+            r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
+            r.dev_off()
+        except Exception, 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] ) )
+
+    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 )
+
+    r.quit( save="no" )
+
+if __name__ == "__main__":
+    main()
diff -r 000000000000 -r c12b0759203b scatterplot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scatterplot.xml	Mon Jul 28 11:56:22 2014 -0400
@@ -0,0 +1,71 @@
+<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.0">
+  <description>of two numeric columns</description>
+  <requirements>
+    <requirement type="package" version="1.0.3">rpy</requirement>
+  </requirements>
+  <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</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" />
+    <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
+    <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
+    <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="out_file1" />
+  </outputs>
+  <!-- TODO: uncomment the following test when we have tools.update_state() working for 
+       multiple dependents with the same dependency.
+  <tests>
+    <test>
+      <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
+      <param name="col1" value="2"/>
+      <param name="col2" value="3"/>
+      <param name="title" value="Scatterplot"/>
+      <param name="xlab" value="V1"/>
+      <param name="ylab" value="V2"/>
+      <output name="out_file1" file="scatterplot_out1.pdf" />
+    </test>
+  </tests>
+  -->
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+
+-----
+
+**Syntax**
+
+This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset. 
+
+- All invalid, blank and comment lines in the dataset are skipped.  The number of skipped lines is displayed in the resulting history item.
+
+- **Plot title** The scatterplot title
+- **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot.
+
+-----
+
+**Example**
+
+- Input file::
+
+    1   68  4.1
+    2   71  4.6
+    3   62  3.8
+    4   75  4.4
+    5   58  3.2
+    6   60  3.1
+    7   67  3.8
+    8   68  4.1
+    9   71  4.3
+    10  69  3.7 
+
+- Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset.
+
+.. image:: scatterplot.png
+
+</help>
+</tool>
diff -r 000000000000 -r c12b0759203b test-data/scatterplot_in1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scatterplot_in1.tabular	Mon Jul 28 11:56:22 2014 -0400
@@ -0,0 +1,10 @@
+1	68	4.1
+2	71	4.6
+3	62	3.8
+4	75	4.4
+5	58	3.2
+6	60	3.1
+7	67	3.8
+8	68	4.1
+9	71	4.3
+10	69	3.7
diff -r 000000000000 -r c12b0759203b test-data/scatterplot_out1.pdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scatterplot_out1.pdf	Mon Jul 28 11:56:22 2014 -0400
@@ -0,0 +1,169 @@
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diff -r 000000000000 -r c12b0759203b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jul 28 11:56:22 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="rpy" version="1.0.3">
+      <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>