From fb569d3c43f00fa8b9bae1a5328c3a5878e37493 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 18 Oct 2007 17:29:47 +0000
Subject: [PATCH] More ColumnListParameter cleanup.  Eliminated dynamic options
 from some tools by using ColumnListParameter.

---
 tools/filters/compare.xml      | 21 ++++++++-------------
 tools/filters/countColumns.py  | 16 ----------------
 tools/filters/joiner.xml       | 13 ++++---------
 tools/filters/joiner2.py       | 16 ----------------
 tools/filters/joiner2.xml      | 13 ++++---------
 tools/filters/sorter.xml       |  2 +-
 tools/filters/uniq.xml         |  2 +-
 tools/plotting/histogram2.xml  |  2 +-
 tools/plotting/scatterplot.xml |  4 ++--
 tools/plotting/xy_plot.xml     | 26 ++++++--------------------
 tools/stats/cor.xml            |  2 +-
 tools/stats/grouping.xml       |  4 ++--
 12 files changed, 30 insertions(+), 91 deletions(-)
 delete mode 100644 tools/filters/countColumns.py
 delete mode 100644 tools/filters/joiner2.py

diff --git a/tools/filters/compare.xml b/tools/filters/compare.xml
index 1de9a1b5464..b18169c3333 100644
--- a/tools/filters/compare.xml
+++ b/tools/filters/compare.xml
@@ -2,23 +2,18 @@
   <description>to find common or distinct rows</description>
   <command interpreter="perl">joinWrapper.pl $input1 $input2 $field1 $field2 $mode "Y" $out_file1</command>
   <inputs>
-    <page>
-      <param format="tabular" name="input1" type="data" label="Compare"/>
-      <param format="tabular" name="input2" type="data" label="against" help="Click [Next Step] to select columns and return type" />
-    </page>
-    <page>
-      <param name="field1" label="Using column" size="4" type="select" dynamic_options="get_available_columns( input1.file_name )" help="of First query"/>
-      <param name="field2" label="and column" size="4" type="select" dynamic_options="get_available_columns( input2.file_name )" help="of Second query"/>
-      <param name="mode" type="select" label="To find" help="See examples below for explanation of these options">
-	<option value="N">Matching rows of 1st query</option>
-	<option value="V">Non Matching rows of 1st query</option>
-      </param>
-    </page>
+    <param format="tabular" name="input1" type="data" label="Compare"/>
+    <param name="field1" label="Using column" type="data_column" data_ref="input1" />
+    <param format="tabular" name="input2" type="data" label="against" />
+    <param name="field2" label="and column" type="data_column" data_ref="input2" />
+    <param name="mode" type="select" label="To find" help="See examples below for explanation of these options">
+      <option value="N">Matching rows of 1st query</option>
+      <option value="V">Non Matching rows of 1st query</option>
+    </param>
   </inputs>
   <outputs>
      <data format="input" name="out_file1" metadata_source="input1" />
   </outputs>
-  <code file="countColumns.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed"/>
diff --git a/tools/filters/countColumns.py b/tools/filters/countColumns.py
deleted file mode 100644
index 0c20cfc2660..00000000000
--- a/tools/filters/countColumns.py
+++ /dev/null
@@ -1,16 +0,0 @@
-#return lists of columns available
-def get_available_columns( input_filename ):
-    rval = []
-    elems = []
-    
-    file_in = open(input_filename, 'r')
-    oneline =  file_in.readline()
-    if oneline :
-        elems = oneline.split('\t')
-    file_in.close() 
-    ncol = len(elems)
-    while ncol > 0:
-        rval.append( (str(ncol), str(ncol), True) )
-	ncol = ncol -1
-	
-    return rval
diff --git a/tools/filters/joiner.xml b/tools/filters/joiner.xml
index c5ea2444882..66739d8dfe3 100644
--- a/tools/filters/joiner.xml
+++ b/tools/filters/joiner.xml
@@ -2,19 +2,14 @@
   <description>side by side on a specified field</description>
   <command interpreter="perl">joinWrapper.pl $input1 $input2 $field1 $field2 "N" "N" $out_file1</command>
   <inputs>
-    <page>
-      <param format="tabular" name="input1" type="data" label="Join"/>
-      <param format="tabular" name="input2" type="data" label="with" help="Click [Next Step] to select columns"/>
-    </page>
-    <page>
-      <param name="field1" label="Using column" size="4" type="select" dynamic_options="get_available_columns( input1.file_name )" help="of First query"/>
-      <param name="field2" label="and column" size="4" type="select" dynamic_options="get_available_columns( input2.file_name )" help="of Second query"/>
-    </page>
+    <param format="tabular" name="input1" type="data" label="Join"/>
+    <param name="field1" label="using column" type="data_column" data_ref="input1" />
+    <param format="tabular" name="input2" type="data" label="with" />
+    <param name="field2" label="and column" type="data_column" data_ref="input2" />
   </inputs>
   <outputs>
      <data format="tabular" name="out_file1" metadata_source="input1" />
   </outputs>
-  <code file="countColumns.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed"/>
diff --git a/tools/filters/joiner2.py b/tools/filters/joiner2.py
deleted file mode 100644
index 0c20cfc2660..00000000000
--- a/tools/filters/joiner2.py
+++ /dev/null
@@ -1,16 +0,0 @@
-#return lists of columns available
-def get_available_columns( input_filename ):
-    rval = []
-    elems = []
-    
-    file_in = open(input_filename, 'r')
-    oneline =  file_in.readline()
-    if oneline :
-        elems = oneline.split('\t')
-    file_in.close() 
-    ncol = len(elems)
-    while ncol > 0:
-        rval.append( (str(ncol), str(ncol), True) )
-	ncol = ncol -1
-	
-    return rval
diff --git a/tools/filters/joiner2.xml b/tools/filters/joiner2.xml
index 0a6cd4f06c0..66aedfc741a 100644
--- a/tools/filters/joiner2.xml
+++ b/tools/filters/joiner2.xml
@@ -2,17 +2,12 @@
   <description>two Queries A specific column of which has the same value</description>
   <command>sort -k $col1 $input1 > $input1.tmp; sort -k $col2 $input2 > $input2.tmp; join -1 $col1 -2 $col2 $input1.tmp $input2.tmp | tr " " "\t" > $out_file1; rm -rf $input1.tmp $input2.tmp </command>
   <inputs>
-    <page>
-    <param name="input1" 	label="Combine Query1" 	format = "tabular" type="data" />
-    <param name="input2" 	label="With Query2"	format = "tabular" type="data"/>
-    </page>
-    <page>
-    <param name="col1"	label="Query 1 on column" size="9" type="select" dynamic_options="get_available_columns( input1.file_name )" />
-    <param name="col2"	label="Query 2 on column" size="9" type="select" dynamic_options="get_available_columns( input2.file_name )" />
-    </page>
+    <param name="input1" label="Combine query" format="tabular" type="data" />
+    <param name="col1" label="using column" type="data_column" data_ref="input1" />
+    <param name="input2" label="with query"	format="tabular" type="data"/>
+    <param name="col2" label="and column" type="data_column" data_ref="input2" />
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input1" />
   </outputs>
-  <code file="joiner2.py"/>
 </tool>
diff --git a/tools/filters/sorter.xml b/tools/filters/sorter.xml
index 3198e0d8ab3..1929af89d79 100644
--- a/tools/filters/sorter.xml
+++ b/tools/filters/sorter.xml
@@ -3,7 +3,7 @@
   <command interpreter="python">sorter.py -i $input -o $out_file1 -cols $column -order $order -style $style</command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Sort Query" />
-    <param name="column" label="on column" type="columnlist" assoc_dataset="input" />
+    <param name="column" label="on column" type="data_column" data_ref="input" />
     <param name="order" type="select" label="in">
       <option value="ASC">Ascending order</option>
       <option value="DESC">Descending order</option>
diff --git a/tools/filters/uniq.xml b/tools/filters/uniq.xml
index 8d3dd9d051b..76060b80f86 100644
--- a/tools/filters/uniq.xml
+++ b/tools/filters/uniq.xml
@@ -3,7 +3,7 @@
   <command interpreter="python">uniq.py -i $input -o $out_file1 -c "$column" -d $delim</command>
   <inputs>
     <param name="input" type="data" format="tabular" label="from query" help="Query missing? See TIP below"/>
-    <param name="column" type="columnlist" assoc_dataset="input" multiple="True" numerical="False" label="Count occurencies of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
+    <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurencies of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
     <param name="delim" type="select" label="Delimited by">
       <option value="T">Tab</option>
       <option value="Sp">Whitespace</option>
diff --git a/tools/plotting/histogram2.xml b/tools/plotting/histogram2.xml
index 02b7581dff1..dea68ba3b46 100644
--- a/tools/plotting/histogram2.xml
+++ b/tools/plotting/histogram2.xml
@@ -3,7 +3,7 @@
   <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density</command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset" help="Query missing? See TIP below"/>
-    <param name="numerical_column" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for x axis" />
+    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
     <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/>
     <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
     <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/>
diff --git a/tools/plotting/scatterplot.xml b/tools/plotting/scatterplot.xml
index 57573a3f74c..152cf850cbe 100644
--- a/tools/plotting/scatterplot.xml
+++ b/tools/plotting/scatterplot.xml
@@ -3,8 +3,8 @@
   <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="Query missing? See TIP below"/>
-    <param name="col1" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for x axis" />
-    <param name="col2" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for y axis" />
+    <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"/>
diff --git a/tools/plotting/xy_plot.xml b/tools/plotting/xy_plot.xml
index b4dbfcc9d20..0facf68c3a2 100644
--- a/tools/plotting/xy_plot.xml
+++ b/tools/plotting/xy_plot.xml
@@ -3,27 +3,13 @@
   <command interpreter="bash">r_wrapper.sh $script_file</command>
 
   <inputs>
-    
-    <param name="main" type="text" 
-           value="" size="30" 
-           label="Plot Title"/>
-    <param name="xlab" type="text" 
-           value="" size="30"
-           label="Label for x axis"/>
-    <param name="ylab" type="text" 
-           value="" size="30"
-           label="Label for y axis"/>
-    
+    <param name="main" type="text" value="" size="30" label="Plot Title"/>
+    <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
+    <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
     <repeat name="series" title="Series">
-      <param name="input"
-             type="data" format="tabular"
-             label="Dataset"/>
-      <param name="xcol" type="data_column" data_ref="input" 
-             value="1" size="30"
-             label="Column for x axis"/>
-      <param name="ycol" type="data_column" data_ref="input" 
-             value="1" size="30" 
-             label="Column for y axis"/>
+      <param name="input" type="data" format="tabular" label="Dataset"/>
+      <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
+      <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
       <conditional name="series_type">
         <param name="type" type="select" label="Series Type">
           <option value="line" selected="true">Line</option>
diff --git a/tools/stats/cor.xml b/tools/stats/cor.xml
index cdb90aa91c4..2e52c396d52 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" help="Query missing? See TIP below"/>
-    <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="numeric_columns" label="Numerical columns" type="data_column" numerical="True" multiple="True" data_ref="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>
diff --git a/tools/stats/grouping.xml b/tools/stats/grouping.xml
index d3969585631..3ab396ac1d0 100644
--- a/tools/stats/grouping.xml
+++ b/tools/stats/grouping.xml
@@ -12,7 +12,7 @@
   </command>
   <inputs>
     <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
-    <param name="groupcol" label="Group by column" type="columnlist" assoc_dataset="input1" />
+    <param name="groupcol" label="Group by column" type="data_column" data_ref="input1" />
     <repeat name="operations" title="Operation">
       <param name="optype" type="select" label="Type">
         <option value="mean">Mean</option>
@@ -21,7 +21,7 @@
         <option value="sum">Sum</option>
         <option value="c">Concatenate</option>
       </param>
-      <param name="opcol" label="On column" type="columnlist" assoc_dataset="input1" />
+      <param name="opcol" label="On column" type="data_column" data_ref="input1" />
   	</repeat>
   </inputs>
   <outputs>