# HG changeset patch
# User iuc
# Date 1638656508 0
# Node ID 9ca2541369b8564fc26d783092078b8bb1fcddc0
# Parent  6d8ee8b7acdafe28fe7133b4cf62b2301228fffa
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 1232893782204bb041dd6ed46711295cb0bfc03f"

diff -r 6d8ee8b7acda -r 9ca2541369b8 varscan.py
--- a/varscan.py	Fri Aug 16 15:48:44 2019 -0400
+++ b/varscan.py	Sat Dec 04 22:21:48 2021 +0000
@@ -358,8 +358,7 @@
                 self.call, self.error
             )
         else:
-            msg_header = '{0} failed.\n'
-            'No further information about this error is available.\n\n'.format(
+            msg_header = '{0} failed.\nNo further information about this error is available.\n\n'.format(
                 self.call
             )
         return msg_header + self.message
@@ -1045,8 +1044,8 @@
                         if mmqs_diff > max_mmqs_diff:
                             record.filter.add('MMQSdiff')
                         if (
-                            1 -
-                            alt_stats.avg_clipped_len
+                            1
+                            - alt_stats.avg_clipped_len
                             / ref_stats.avg_clipped_len
                         ) > max_relative_len_diff:
                             record.filter.add('ReadLenDiff')
diff -r 6d8ee8b7acda -r 9ca2541369b8 varscan_copynumber.xml
--- a/varscan_copynumber.xml	Fri Aug 16 15:48:44 2019 -0400
+++ b/varscan_copynumber.xml	Sat Dec 04 22:21:48 2021 +0000
@@ -41,8 +41,6 @@
         <param argument="--data-ratio" name="data_ratio" type="float" value="1.0" min="0.0" max="1.0"
             label="The normal/tumor input data ratio for copynumber adjustment"/>
 
-        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
-
     </inputs>
     <outputs>
         <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/>