# HG changeset patch
# User peterjc
# Date 1550848451 18000
# Node ID 8ceccb6738de650e8acd653eac858eb496d5b2d3
# Parent  9e02126950942a87de255505d41f442b7232dd77
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty

diff -r 9e0212695094 -r 8ceccb6738de tools/fastq_pair_names/fastq_pair_names.py
--- a/tools/fastq_pair_names/fastq_pair_names.py	Fri Nov 09 10:52:02 2018 -0500
+++ b/tools/fastq_pair_names/fastq_pair_names.py	Fri Feb 22 10:14:11 2019 -0500
@@ -70,8 +70,12 @@
 re_illumina_r = re.compile(r"^@[a-zA-Z0-9_:-]+ 2:.*$")
 assert re_illumina_f.match("@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA")
 assert re_illumina_r.match("@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA")
-assert not re_illumina_f.match("@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA")
-assert not re_illumina_r.match("@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA")
+assert not re_illumina_f.match(
+    "@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA"
+)
+assert not re_illumina_r.match(
+    "@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA"
+)
 
 count = 0
 pairs = set()  # Will this scale OK?
@@ -99,7 +103,7 @@
             # ============
             # Forward read
             # ============
-            template = name[:suffix.start()]
+            template = name[: suffix.start()]
             is_forward = True
         elif re_illumina_f.match(record.identifier):
             template = name  # No suffix
@@ -116,7 +120,7 @@
                 # ============
                 # Reverse read
                 # ============
-                template = name[:suffix.start()]
+                template = name[: suffix.start()]
                 is_reverse = True
             elif re_illumina_r.match(record.identifier):
                 template = name  # No suffix
@@ -136,5 +140,7 @@
 out_pairs.close()
 out_nonpairs.close()
 
-print("%i reads (%i forward, %i reverse, %i neither), %i pairs" %
-      (count, forward, reverse, neither, len(pairs)))
+print(
+    "%i reads (%i forward, %i reverse, %i neither), %i pairs"
+    % (count, forward, reverse, neither, len(pairs))
+)
diff -r 9e0212695094 -r 8ceccb6738de tools/fastq_pair_names/tool_dependencies.xml
--- a/tools/fastq_pair_names/tool_dependencies.xml	Fri Nov 09 10:52:02 2018 -0500
+++ b/tools/fastq_pair_names/tool_dependencies.xml	Fri Feb 22 10:14:11 2019 -0500
@@ -1,6 +1,6 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="galaxy_sequence_utils" version="1.0.1">
-        <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file