# HG changeset patch
# User bgruening
# Date 1531468618 14400
# Node ID bf3a5f8a66a2f87545e941aa9d308d3e4fd2d9db
# Parent f2707c822dee6fe78b23031d3a6ca698d7e47fcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
diff -r f2707c822dee -r bf3a5f8a66a2 main_macros.xml
--- a/main_macros.xml Tue Jul 10 03:13:29 2018 -0400
+++ b/main_macros.xml Fri Jul 13 03:56:58 2018 -0400
@@ -35,7 +35,8 @@
if not options['threshold'] or options['threshold'] == 'None':
options['threshold'] = None
if 'extra_estimator' in inputs and inputs['extra_estimator']['has_estimator'] == 'no_load':
- fitted_estimator = pickle.load(open("inputs['extra_estimator']['fitted_estimator']", 'r'))
+ with open("inputs['extra_estimator']['fitted_estimator']", 'rb') as model_handler:
+ fitted_estimator = pickle.load(model_handler)
new_selector = selector(fitted_estimator, prefit=True, **options)
else:
estimator=inputs["estimator"]
@@ -83,7 +84,7 @@
parse_dates=True
)
else:
- X = mmread(open(file1, 'r'))
+ X = mmread(file1)
header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None
column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
@@ -432,19 +433,6 @@
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diff -r f2707c822dee -r bf3a5f8a66a2 sparse.xml
--- a/sparse.xml Tue Jul 10 03:13:29 2018 -0400
+++ b/sparse.xml Fri Jul 13 03:56:58 2018 -0400
@@ -24,18 +24,20 @@
from scipy.io import mmwrite
input_json_path = sys.argv[1]
-params = json.load(open(input_json_path, "r"))
+with open(input_json_path, "r") as param_handler:
+ params = json.load(param_handler)
sparse_iter = []
#for $i, $s in enumerate( $sparse_functions.sparse_inputs )
sparse_index=$i
sparse_path="${s.input.file_name}"
-sparse_iter.append(mmread(open(sparse_path, 'r')))
+sparse_iter.append(mmread(sparse_path))
#end for
my_function = getattr(sparse, params["sparse_functions"]["selected_function"])
my_sparse = my_function(sparse_iter)
-mmwrite(open("$outfile", 'w+'), my_sparse)
+with open("$outfile", "w+") as out_handler:
+ mmwrite(out_handler, my_sparse)
]]>
diff -r f2707c822dee -r bf3a5f8a66a2 test-data/mv_result07.tabular
--- a/test-data/mv_result07.tabular Tue Jul 10 03:13:29 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-0.7824428015300172