details: http://www.bx.psu.edu/hg/galaxy/rev/4d4de72c57c8 changeset: 1732:4d4de72c57c8 user: guru date: Tue Feb 03 15:06:21 2009 -0500 description: Removed lzo requirement from two tools- getIndels and qualityFilter. Also added validator to the regression tools.
5 file(s) affected in this change:
tools/regVariation/best_regression_subsets.xml tools/regVariation/getIndels.py tools/regVariation/linear_regression.xml tools/regVariation/quality_filter.py tools/regVariation/rcve.xml
diffs (94 lines):
diff -r e26741c8c642 -r 4d4de72c57c8 tools/regVariation/best_regression_subsets.xml --- a/tools/regVariation/best_regression_subsets.xml Tue Feb 03 14:15:09 2009 -0500 +++ b/tools/regVariation/best_regression_subsets.xml Tue Feb 03 15:06:21 2009 -0500 @@ -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 -r e26741c8c642 -r 4d4de72c57c8 tools/regVariation/getIndels.py --- a/tools/regVariation/getIndels.py Tue Feb 03 14:15:09 2009 -0500 +++ b/tools/regVariation/getIndels.py Tue Feb 03 15:06:21 2009 -0500 @@ -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 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 -r e26741c8c642 -r 4d4de72c57c8 tools/regVariation/linear_regression.xml --- a/tools/regVariation/linear_regression.xml Tue Feb 03 14:15:09 2009 -0500 +++ b/tools/regVariation/linear_regression.xml Tue Feb 03 15:06:21 2009 -0500 @@ -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 -r e26741c8c642 -r 4d4de72c57c8 tools/regVariation/quality_filter.py --- a/tools/regVariation/quality_filter.py Tue Feb 03 14:15:09 2009 -0500 +++ b/tools/regVariation/quality_filter.py Tue Feb 03 15:06:21 2009 -0500 @@ -12,11 +12,7 @@ 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 -r e26741c8c642 -r 4d4de72c57c8 tools/regVariation/rcve.xml --- a/tools/regVariation/rcve.xml Tue Feb 03 14:15:09 2009 -0500 +++ b/tools/regVariation/rcve.xml Tue Feb 03 15:06:21 2009 -0500 @@ -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" />