# HG changeset patch
# User peterjc
# Date 1559582893 14400
# Node ID e28d6015fc564071a1702446a6a974f96c5a7f50
# Parent  85b86f31327c4a685669d8beb005c074c5be30f7
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 89578746a1c5b29c84a173d8b2709f086f69a7b6

diff -r 85b86f31327c -r e28d6015fc56 tools/mira3/mira.py
--- a/tools/mira3/mira.py	Wed Jul 11 12:34:58 2018 -0400
+++ b/tools/mira3/mira.py	Mon Jun 03 13:28:13 2019 -0400
@@ -18,9 +18,12 @@
     # however there is some pipe error when doing that here.
     cmd = ["mira", "-v"]
     try:
-        child = subprocess.Popen(cmd, universal_newlines=True,
-                                 stdout=subprocess.PIPE,
-                                 stderr=subprocess.STDOUT)
+        child = subprocess.Popen(
+            cmd,
+            universal_newlines=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+        )
     except Exception as err:
         sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
         sys.exit(1)
@@ -45,11 +48,13 @@
     if not os.listdir(f):
         sys.exit("Empty output folder")
     missing = []
-    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
-                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
-                     ("%s/%s_out.wig" % (f, name), out_wig),
-                     ("%s/%s_out.caf" % (f, name), out_caf),
-                     ("%s/%s_out.ace" % (f, name), out_ace)]:
+    for old, new in [
+        ("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
+        ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
+        ("%s/%s_out.wig" % (f, name), out_wig),
+        ("%s/%s_out.caf" % (f, name), out_caf),
+        ("%s/%s_out.ace" % (f, name), out_ace),
+    ]:
         if not os.path.isfile(old):
             missing.append(os.path.splitext(old)[-1])
         else:
@@ -90,9 +95,9 @@
 handle = open(out_log, "w")
 try:
     # Run MIRA
-    child = subprocess.Popen(cmd_list, universal_newlines=True,
-                             stdout=handle,
-                             stderr=subprocess.STDOUT)
+    child = subprocess.Popen(
+        cmd_list, universal_newlines=True, stdout=handle, stderr=subprocess.STDOUT
+    )
 except Exception as err:
     sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
     # TODO - call clean up?
diff -r 85b86f31327c -r e28d6015fc56 tools/mira3/tool_dependencies.xml
--- a/tools/mira3/tool_dependencies.xml	Wed Jul 11 12:34:58 2018 -0400
+++ b/tools/mira3/tool_dependencies.xml	Mon Jun 03 13:28:13 2019 -0400
@@ -1,6 +1,6 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="MIRA" version="3.4.1.1">
-        <repository changeset_revision="aff5e2528b9d" name="package_mira_3_4_1_1" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="aff5e2528b9d" name="package_mira_3_4_1_1" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file