Removed lzo requirement from two tools- getIndels and qualityFilter.

Also added validator to the regression tools.

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" />

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

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" />

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

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" />