diff test.py @ 0:629e7e403e19 draft

"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.py	Thu Jul 01 11:36:43 2021 +0000
@@ -0,0 +1,60 @@
+import argparse
+import os
+from shutil import copyfile
+
+#immuneml --inputs file1 file2 file3 --output_dir /some/path --yaml_path abc.yml --metadata abc.csv --tool galaxy_yaml_tool
+
+def get_args():
+    parser = argparse.ArgumentParser(description='Tool for detecting known and novel MicroRNAs')
+    parser.add_argument('-o', '--output_dir', help='Output directory', default='.', required=True)
+    parser.add_argument('-i', '--inputs', help='Input directory', default='.', required=True, nargs='+')
+    parser.add_argument('-y', '--yaml', help='Yaml input', default='.', required=True)
+    parser.add_argument('-m', '--metadata', help='Metadata input', default='.', required=False)
+    parser.add_argument('-t', '--tool', help='Tool', default='.', required=False)
+
+    return parser.parse_args()
+
+
+def main():
+    print('main')
+    args = get_args()
+
+    print(args.output_dir)
+    print(args.inputs)
+
+    #os.mkdir(args.output_dir)
+    i = 0
+    html_files_links = ''
+    for f in args.inputs:
+        filename = str(i) + '.txt'
+        copyfile(f, os.path.join(args.output_dir, str(i) + '.txt'))
+        i += 1
+        html_files_links += '<li><a href="' + filename + '" title="' + filename + '">Input file ' + str(i) + '</a></li>'
+
+    copyfile(args.yaml, os.path.join(args.output_dir, 'yaml_file.txt'))
+    copyfile(args.metadata, os.path.join(args.output_dir, 'metadata_file.txt'))
+    copyfile('pipout.txt', os.path.join(args.output_dir, 'pipout.txt'))
+    copyfile('immuneout.txt', os.path.join(args.output_dir, 'immuneout.txt'))
+    html_files_links += '<li><a href="yaml_file.txt" title="YAML file">YAML file</a></li>'
+    html_files_links += '<li><a href="metadata_file.txt" title="Metadata file">Metadata file</a></li>'
+    html_files_links += '<li><a href="pipout.txt" title="Pip output">Pip output</a></li>'
+    html_files_links += '<li><a href="immuneout.txt" title="ImmuneML output">ImmuneML output</a></li>'
+
+    html_output = open(os.path.join(args.output_dir, 'output.html'), 'w')
+
+    html_test = '''<nav>
+    <ul>'''
+
+    html_test += html_files_links
+    html_test += '''</ul>
+    </nav>'''
+    html_output.write(html_test)
+    html_output.close()
+
+
+if __name__ == '__main__':
+    main()
+
+
+
+