Mercurial > repos > devteam > macs
changeset 2:5d67bc6f385f 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 15:28:57 +0000 |
| parents | 7f4aca133f73 |
| children | |
| files | macs_wrapper.py macs_wrapper.xml tool_dependencies.xml |
| diffstat | 3 files changed, 10 insertions(+), 9 deletions(-) [+] |
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--- a/macs_wrapper.py Tue Oct 13 12:24:35 2015 -0400 +++ b/macs_wrapper.py Wed Feb 05 15:28:57 2020 +0000 @@ -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 Tue Oct 13 12:24:35 2015 -0400 +++ b/macs_wrapper.xml Wed Feb 05 15:28:57 2020 +0000 @@ -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 Tue Oct 13 12:24:35 2015 -0400 +++ b/tool_dependencies.xml Wed Feb 05 15:28:57 2020 +0000 @@ -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="3e6290791f9c" name="package_macs_1_3_7_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="macs" version="1.3.7.1"> + <repository changeset_revision="3e6290791f9c" name="package_macs_1_3_7_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </package> <package name="R" version="2.15.0"> - <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file