Move CONVERTER_fastq_to_fqtoc0 out of GALAXY_LIB_TOOLS_UNVERSIONED

lib/galaxy/datatypes/converters/fastq_to_fqtoc.py

@@ -20,30 +20,26 @@ def main():
     """
     input_fname = sys.argv[1]
     if is_gzip(input_fname):
-        print('Conversion is only possible for uncompressed files')
-        sys.exit(1)
-
-    out_file = open(sys.argv[2], 'w')
+        sys.exit('Conversion is only possible for uncompressed files')
 
     current_line = 0
     sequences = 1000000
     lines_per_chunk = 4 * sequences
     chunk_begin = 0
 
-    in_file = open(input_fname)
+    with open(input_fname) as in_file, open(sys.argv[2], 'w') as out_file:
+        out_file.write('{"sections" : [')
 
-    out_file.write('{"sections" : [')
+        for line in in_file:
+            current_line += 1
+            if 0 == current_line % lines_per_chunk:
+                chunk_end = in_file.tell()
+                out_file.write('{"start":"%s","end":"%s","sequences":"%s"},' % (chunk_begin, chunk_end, sequences))
+                chunk_begin = chunk_end
 
-    for line in in_file:
-        current_line += 1
-        if 0 == current_line % lines_per_chunk:
-            chunk_end = in_file.tell()
-            out_file.write('{"start":"%s","end":"%s","sequences":"%s"},' % (chunk_begin, chunk_end, sequences))
-            chunk_begin = chunk_end
-
-    chunk_end = in_file.tell()
-    out_file.write('{"start":"%s","end":"%s","sequences":"%s"}' % (chunk_begin, chunk_end, (current_line % lines_per_chunk) / 4))
-    out_file.write(']}\n')
+        chunk_end = in_file.tell()
+        out_file.write('{"start":"%s","end":"%s","sequences":"%s"}' % (chunk_begin, chunk_end, (current_line % lines_per_chunk) / 4))
+        out_file.write(']}\n')
 
 
 if __name__ == "__main__":

lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml

@@ -1,4 +1,7 @@
-<tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.0" hidden="true">
+<tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.1" hidden="true" profile="16.04">
+    <requirements>
+        <requirement type="package" version="19.09">galaxy-util</requirement>
+    </requirements>
     <command>python '$__tool_directory__/fastq_to_fqtoc.py' '$input1' '$output1'</command>
     <inputs>
         <param format="fastq" name="input1" type="data" label="Choose FASTQ file"/>

lib/galaxy/tools/__init__.py

@@ -144,7 +144,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "maf_by_block_number1",
     # Converters
     "CONVERTER_bed_to_fli_0",
-    "CONVERTER_fastq_to_fqtoc0",
     "CONVERTER_gff_to_fli_0",
     "CONVERTER_gff_to_interval_index_0",
     "CONVERTER_maf_to_fasta_0",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "wiggle2simple1": packaging.version.parse("1.0.1"),
     "CONVERTER_wiggle_to_interval_0": packaging.version.parse("1.0.1"),
     "aggregate_scores_in_intervals2": packaging.version.parse("1.1.4"),
+    "CONVERTER_fastq_to_fqtoc0": packaging.version.parse("1.0.1"),
 }