Move wiggle_to_interval out of GALAXY_LIB_TOOLS_UNVERSIONED

lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py

@@ -11,40 +11,20 @@ import sys
 
 import bx.wiggle
 
-from galaxy.util import unicodify
 from galaxy.util.ucsc import (
     UCSCLimitException,
     UCSCOutWrapper
 )
 
 
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
-
-
 def main():
-    if len(sys.argv) > 1:
-        in_file = open(sys.argv[1])
-    else:
-        in_file = open(sys.stdin)
-
-    if len(sys.argv) > 2:
-        out_file = open(sys.argv[2], "w")
-    else:
-        out_file = sys.stdout
-
-    try:
-        for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-            out_file.write("%s\n" % "\t".join(map(str, fields)))
-    except UCSCLimitException:
-        # Wiggle data was truncated, at the very least need to warn the user.
-        print('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
-    except ValueError as e:
-        stop_err(unicodify(e))
-    finally:
-        in_file.close()
-        out_file.close()
+    with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
+        try:
+            for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
+                out_file.write("%s\n" % "\t".join(map(str, fields)))
+        except UCSCLimitException:
+            # Wiggle data was truncated, at the very least need to warn the user.
+            sys.stderr.write('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
 
 
 if __name__ == "__main__":

lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml

@@ -1,6 +1,10 @@
-<tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval" version="1.0.0">
+<tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+      <requirement type="package" version="19.09">galaxy-util</requirement>
+      <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/wiggle_to_simple_converter.py' '$input' '$out_file1'</command>
     <inputs>
         <param format="wig" name="input" type="data" label="Convert"/>

lib/galaxy/tools/__init__.py

@@ -143,7 +143,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "MAF_split_blocks_by_species1",
     "MAF_Limit_To_Species1",
     "maf_by_block_number1",
-    "wiggle2simple1",
     # Converters
     "CONVERTER_bed_to_fli_0",
     "CONVERTER_fastq_to_fqtoc0",
@@ -151,7 +150,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "CONVERTER_gff_to_interval_index_0",
     "CONVERTER_maf_to_fasta_0",
     "CONVERTER_maf_to_interval_0",
-    "CONVERTER_wiggle_to_interval_0",
     "CONVERTER_tar_to_directory",
     # Tools improperly migrated to the tool shed (devteam)
     "qualityFilter",
@@ -191,6 +189,8 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "vcf_to_maf_customtrack1": packaging.version.parse("1.0.1"),
     "secure_hash_message_digest": packaging.version.parse("0.0.2"),
     "join1": packaging.version.parse("2.1.3"),
+    "wiggle2simple1": packaging.version.parse("1.0.1"),
+    "CONVERTER_wiggle_to_interval_0": packaging.version.parse("1.0.1"),
 }
 
 

tools/filters/wiggle_to_simple.py

@@ -10,38 +10,20 @@ import sys
 
 import bx.wiggle
 
-from galaxy.util.ucsc import UCSCLimitException, UCSCOutWrapper
-
-
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
+from galaxy.util.ucsc import (
+    UCSCLimitException,
+    UCSCOutWrapper
+)
 
 
 def main():
-    if len(sys.argv) > 1:
-        in_file = open(sys.argv[1])
-    else:
-        in_file = open(sys.stdin)
-
-    if len(sys.argv) > 2:
-        out_file = open(sys.argv[2], "w")
-    else:
-        out_file = sys.stdout
-
-    try:
-        for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-            out_file.write("%s\n" % "\t".join(map(str, fields)))
-    except UCSCLimitException:
-        # Wiggle data was truncated, at the very least need to warn the user.
-        print('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
-    except ValueError as e:
-        in_file.close()
-        out_file.close()
-        stop_err(str(e))
-
-    in_file.close()
-    out_file.close()
+    with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
+        try:
+            for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
+                out_file.write("%s\n" % "\t".join(map(str, fields)))
+        except UCSCLimitException:
+            # Wiggle data was truncated, at the very least need to warn the user.
+            sys.stderr.write('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
 
 
 if __name__ == "__main__":

tools/filters/wiggle_to_simple.xml

@@ -1,6 +1,10 @@
-<tool id="wiggle2simple1" name="Wiggle-to-Interval" version="1.0.0">
+<tool id="wiggle2simple1" name="Wiggle-to-Interval" version="1.0.1" profile="16.04">
   <description>converter</description>
-  <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
+  <requirements>
+    <requirement type="package" version="19.09">galaxy-util</requirement>
+    <requirement type="package" version="0.8.6">bx-python</requirement>
+  </requirements>
+  <command>python '$__tool_directory__/wiggle_to_simple.py' '$input' '$out_file1'</command>
   <inputs>
     <param format="wig" name="input" type="data" label="Convert"/>
   </inputs>