From 41d1ce79c87f4a6a889be855080d8e2ae59cecfa Mon Sep 17 00:00:00 2001
From: Guruprasad Anada <gua110@bx.psu.edu>
Date: Tue, 3 Feb 2009 15:06:21 -0500
Subject: [PATCH] Removed lzo requirement from two tools- getIndels and
 qualityFilter. Also added validator to the regression tools.

---
 tools/regVariation/best_regression_subsets.xml |  4 +++-
 tools/regVariation/getIndels.py                | 16 ++--------------
 tools/regVariation/linear_regression.xml       |  4 +++-
 tools/regVariation/quality_filter.py           |  6 +-----
 tools/regVariation/rcve.xml                    |  4 +++-
 5 files changed, 12 insertions(+), 22 deletions(-)

diff --git a/tools/regVariation/best_regression_subsets.xml b/tools/regVariation/best_regression_subsets.xml
index bf382f86cb7..84c3e3ddf3e 100644
--- a/tools/regVariation/best_regression_subsets.xml
+++ b/tools/regVariation/best_regression_subsets.xml
@@ -13,7 +13,9 @@
   <inputs>
     <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
     <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
-    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" />
+    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" >
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input1" />
diff --git a/tools/regVariation/getIndels.py b/tools/regVariation/getIndels.py
index 81bbb975038..d18b12e912c 100644
--- a/tools/regVariation/getIndels.py
+++ b/tools/regVariation/getIndels.py
@@ -1,7 +1,7 @@
 #!/usr/bin/python
 
 """
-Estimate INDELs for pait-wise alignments.
+Estimate INDELs for pair-wise alignments.
 
 usage: %prog maf_input out_file1 out_file2
 """
@@ -10,22 +10,10 @@ from __future__ import division
 from galaxy import eggs
 import pkg_resources 
 pkg_resources.require( "bx-python" )
-pkg_resources.require( "lrucache" )
-try:
-    pkg_resources.require("numpy")
-    pkg_resources.require( "python-lzo" )
-except:
-    pass
+pkg_resources.require("numpy")
 
 import psyco_full
 import sys
-import os, os.path
-from UserDict import DictMixin
-import bx.wiggle
-from bx.binned_array import BinnedArray, FileBinnedArray
-from bx.bitset import *
-from bx.bitset_builders import *
-from fpconst import isNaN
 from bx.cookbook import doc_optparse
 from galaxy.tools.exception_handling import *
 import bx.align.maf
diff --git a/tools/regVariation/linear_regression.xml b/tools/regVariation/linear_regression.xml
index d4fc74a1271..75c0da55556 100644
--- a/tools/regVariation/linear_regression.xml
+++ b/tools/regVariation/linear_regression.xml
@@ -12,7 +12,9 @@
   <inputs>
     <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
     <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
-    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" />
+    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" >
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input1" />
diff --git a/tools/regVariation/quality_filter.py b/tools/regVariation/quality_filter.py
index d77a296861d..9e0cb06a25f 100644
--- a/tools/regVariation/quality_filter.py
+++ b/tools/regVariation/quality_filter.py
@@ -12,11 +12,7 @@ from galaxy import eggs
 import pkg_resources 
 pkg_resources.require( "bx-python" )
 pkg_resources.require( "lrucache" )
-try:
-    pkg_resources.require("numpy")
-    pkg_resources.require( "python-lzo" )
-except:
-    pass
+pkg_resources.require("numpy")
 
 import psyco_full
 import sys
diff --git a/tools/regVariation/rcve.xml b/tools/regVariation/rcve.xml
index 7fe82e92aca..1d1903cc114 100644
--- a/tools/regVariation/rcve.xml
+++ b/tools/regVariation/rcve.xml
@@ -11,7 +11,9 @@
   <inputs>
     <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
     <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
-    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" />
+    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true">
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input1" />