# HG changeset patch
# User peterjc
# Date 1550848843 18000
# Node ID cf3c85c72c573062e0935f3c8860394a0aa56c8a
# Parent  eb899753409f1c30f8b2c8a990f7c8258173dea6
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty

diff -r eb899753409f -r cf3c85c72c57 tools/samtools_depad/samtools_depad.py
--- a/tools/samtools_depad/samtools_depad.py	Fri Nov 09 11:02:23 2018 -0500
+++ b/tools/samtools_depad/samtools_depad.py	Fri Feb 22 10:20:43 2019 -0500
@@ -22,7 +22,10 @@
     sys.exit(os.system(cmd))
 
 if len(sys.argv) != 5:
-    sys.exit("Require four arguments: padded FASTA, SAM/BAM file, format (SAM or BAM), output BAM filenames")
+    sys.exit(
+        "Require four arguments: padded FASTA, SAM/BAM file, format "
+        "(SAM or BAM), output BAM filenames"
+    )
 
 padded_ref, bam_filename, input_format, output_filename = sys.argv[1:]
 
@@ -35,9 +38,17 @@
 
 # Run samtools depad:
 if input_format.lower() == "sam":
-    cmd = "samtools depad -S -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename)
+    cmd = "samtools depad -S -T '%s' '%s' > '%s'" % (
+        padded_ref,
+        bam_filename,
+        output_filename,
+    )
 else:
-    cmd = "samtools depad -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename)
+    cmd = "samtools depad -T '%s' '%s' > '%s'" % (
+        padded_ref,
+        bam_filename,
+        output_filename,
+    )
 return_code = os.system(cmd)
 
 if return_code:
diff -r eb899753409f -r cf3c85c72c57 tools/samtools_depad/tool_dependencies.xml
--- a/tools/samtools_depad/tool_dependencies.xml	Fri Nov 09 11:02:23 2018 -0500
+++ b/tools/samtools_depad/tool_dependencies.xml	Fri Feb 22 10:20:43 2019 -0500
@@ -1,6 +1,6 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file