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

@@ -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')
 

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|

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>

tools/filters/sorter_code.py

@@ -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

tools/plotting/histogram.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python2.4
+#Greg Von Kuster
 
 import sys
 from rpy import *

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 ):

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>