From 50968827e90a9555fbb06d4c0a82fce9bf26d59c Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 17 Sep 2007 20:48:59 +0000
Subject: [PATCH] Enhanced sort tool to use columnlist tool parameter, altered
 functional test to work with new version.  Some other miscellaneous cleanup.

---
 test/functional/test_3E_Filter.py          |  3 +--
 tools/extract/phastOdds/phastOdds_tool.xml |  2 +-
 tools/filters/sorter.xml                   | 29 +++++++++-------------
 tools/filters/sorter_code.py               |  8 ------
 tools/plotting/histogram.py                |  1 +
 tools/plotting/scatterplot.py              |  2 +-
 tools/stats/cor.xml                        |  2 +-
 7 files changed, 17 insertions(+), 30 deletions(-)
 delete mode 100644 tools/filters/sorter_code.py

diff --git a/test/functional/test_3E_Filter.py b/test/functional/test_3E_Filter.py
index 3825876f7bd..8ec2e439345 100644
--- a/test/functional/test_3E_Filter.py
+++ b/test/functional/test_3E_Filter.py
@@ -34,8 +34,7 @@ class FilterTests(TwillTestCase):
 
     def test_21_Sort1(self):
         """3E_Filter: Sort on column one"""
-        self.run_tool("sort1", input="7.bed")
-        self.submit_form(1, column="1", order="ASC", style="alpha")
+        self.run_tool("sort1", input="7.bed", column="1", order="ASC", style="alpha")
         self.wait()
         self.check_data('sc_3E_sort.bed')
 
diff --git a/tools/extract/phastOdds/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_tool.xml
index 7260fb334ff..7b3084b1b30 100644
--- a/tools/extract/phastOdds/phastOdds_tool.xml
+++ b/tools/extract/phastOdds/phastOdds_tool.xml
@@ -40,7 +40,7 @@ If your original data has the following format:
 |chrom|start|end|
 +-----+-----+---+
 
-and you choose to compute phastCons scores, your output will look like this:
+and you choose to compute phastOdds scores, your output will look like this:
 
 +-----+-----+---+-----+
 |chrom|start|end|score|
diff --git a/tools/filters/sorter.xml b/tools/filters/sorter.xml
index cd7c77d748f..991c316c639 100644
--- a/tools/filters/sorter.xml
+++ b/tools/filters/sorter.xml
@@ -2,20 +2,16 @@
   <description>data in ascending or descending order</description>
   <command interpreter="python">sorter.py -i $input -o $out_file1 -cols $column -order $order -style $style</command>
   <inputs>
-    <page>
-      <param format="tabular" name="input" type="data" label="Sort Query"/>
-    </page>
-    <page>
-      <param name="column" label="on column" type="select" dynamic_options="get_columns( input )" />
-      <param name="order" type="select" label="in">
-        <option value="ASC">Ascending order</option>
-        <option value="DESC">Descending order</option>
-      </param>
-      <param name="style" type="select" label="Flavor">
-        <option value="alpha">Alphabetical sort</option>
-        <option value="num">Numerical sort</option>
-      </param>
-    </page>
+    <param format="tabular" name="input" type="data" label="Sort Query" refresh_on_change="True" />
+    <param name="column" label="on column" type="columnlist" assoc_dataset="input" />
+    <param name="order" type="select" label="in">
+      <option value="ASC">Ascending order</option>
+      <option value="DESC">Descending order</option>
+    </param>
+    <param name="style" type="select" label="Flavor">
+      <option value="alpha">Alphabetical sort</option>
+      <option value="num">Numerical sort</option>
+    </param>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input"/>
@@ -23,7 +19,7 @@
   <tests>
     <test>
       <param name="input" value="1.bed"/>
-      <param name="column" value="c1"/>
+      <param name="column" value="1"/>
       <param name="order" value="ASC"/>
       <param name="style" value="num"/>
       <output name="out_file1" file="fs-sort.dat"/>
@@ -50,6 +46,5 @@ This tool sorts the dataset on any column in either ascending or descending orde
 
 The list of numbers 4,17,3,5 collates to 3,4,5,17 by numerical sorting, while it collates to 17,3,4,5 by alphabetical sorting.
 
-</help>
-  <code file="sorter_code.py"/>
+  </help>
 </tool>
diff --git a/tools/filters/sorter_code.py b/tools/filters/sorter_code.py
deleted file mode 100644
index 6477df1b695..00000000000
--- a/tools/filters/sorter_code.py
+++ /dev/null
@@ -1,8 +0,0 @@
-
-def get_columns( input1 ):
-    columns = []
-
-    for col in range(1, input1.metadata.columns+1):
-        option = "c" + str(col)
-        columns.append((option,str(col),False))
-    return columns
\ No newline at end of file
diff --git a/tools/plotting/histogram.py b/tools/plotting/histogram.py
index c7a5d36f9e7..ab022c9da78 100644
--- a/tools/plotting/histogram.py
+++ b/tools/plotting/histogram.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python2.4
+#Greg Von Kuster
 
 import sys
 from rpy import *
diff --git a/tools/plotting/scatterplot.py b/tools/plotting/scatterplot.py
index 82e452c2633..f082eb9ff48 100644
--- a/tools/plotting/scatterplot.py
+++ b/tools/plotting/scatterplot.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
+#Greg Von Kuster
 
 import sys
-from Numeric import *
 from rpy import *
 
 def fail( message ):
diff --git a/tools/stats/cor.xml b/tools/stats/cor.xml
index ca832027582..d69ba6652a6 100644
--- a/tools/stats/cor.xml
+++ b/tools/stats/cor.xml
@@ -3,7 +3,7 @@
   <command interpreter="python">cor.py $input1 $out_file1 $numeric_columns $method</command>
   <inputs>
     <param format="tabular" name="input1" type="data" label="Dataset" refresh_on_change="True" help="Query missing? See TIP below"/>
-    <param name="numeric_columns" label="Numeric columns" type="columnlist" numerical="True" multiple="True" assoc_dataset="input1" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
+    <param name="numeric_columns" label="Numerical columns" type="columnlist" numerical="True" multiple="True" assoc_dataset="input1" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
     <param name="method" type="select" label="Method">
       <option value="pearson">Pearson</option>
       <option value="kendall">Kendall rank</option>