changeset 3:e5f3bfba6812 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/macs commit 206cd8245e7619b0e924c5066d0172129222993d"
author devteam
date Wed, 05 Feb 2020 10:28:23 -0500
parents f6319b0b4391
children
files macs_wrapper.py macs_wrapper.xml tool_dependencies.xml
diffstat 3 files changed, 10 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/macs_wrapper.py	Wed Nov 11 12:19:24 2015 -0500
+++ b/macs_wrapper.py	Wed Feb 05 10:28:23 2020 -0500
@@ -122,14 +122,14 @@
             os.rmdir( wig_base_dir )
     
     #move all remaining files to extra files path of html file output to allow user download
-    out_html = open( output_extra_html, 'wb' )
+    out_html = open( output_extra_html, 'w' )
     out_html.write( '<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name )
     os.mkdir( output_extra_path )
     for filename in sorted( os.listdir( tmp_dir ) ):
         shutil.move( os.path.join( tmp_dir, filename ), os.path.join( output_extra_path, filename ) )
         out_html.write( '<li><a href="%s">%s</a></li>\n' % ( filename, filename ) )
     out_html.write( '</ul></p>\n' )
-    out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'rb' ).read() )
+    out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'r' ).read() )
     out_html.write( '</body></html>\n' )
     out_html.close()
     
--- a/macs_wrapper.xml	Wed Nov 11 12:19:24 2015 -0500
+++ b/macs_wrapper.xml	Wed Feb 05 10:28:23 2020 -0500
@@ -1,6 +1,7 @@
-<tool id="peakcalling_macs" name="MACS" version="1.0.1">
+<tool id="peakcalling_macs" name="MACS" version="1.0.1" profile="16.04">
   <description>Model-based Analysis of ChIP-Seq</description>
-  <command interpreter="python">macs_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path</command>
+  <command>
+  python '$__tool_directory__/macs_wrapper.py' '$options_file' '$output_bed_file' '$output_extra_files' '$output_extra_files.files_path'</command>
   <requirements>
     <requirement type="package" version="1.3.7.1">macs</requirement>
     <requirement type="package" version="2.15.0">R</requirement>
--- a/tool_dependencies.xml	Wed Nov 11 12:19:24 2015 -0500
+++ b/tool_dependencies.xml	Wed Feb 05 10:28:23 2020 -0500
@@ -1,9 +1,9 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
-  <package name="macs" version="1.3.7.1">
-      <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="macs" version="1.3.7.1">
+        <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="R" version="2.15.0">
-      <repository changeset_revision="6c34eaa82fed" name="package_r_2_15_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="6c34eaa82fed" name="package_r_2_15_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
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