make_tep.py – Makes TopiaryExplorer project file¶
Description:
This script makes a TopiaryExplorer project file (.tep) and a jnlp file with the data location preloaded.
WARNING: The jnlp file relies on an absolute path, if you move the .tep file, the generated jnlp will no longer work. However, you can still open the .tep file from your normal TopiaryExplorer install.
Usage: make_tep.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --otu_table_fp
- Path to the input OTU table (i.e., the output from make_otu_table.py)
- -m, --mapping_fp
- The mapping filepath
- -t, --tree_fp
- Path to tree
[OPTIONAL]
- -o, --output_dir
- Path to the output directory
- -p, --prefs_file_fp
- Path to prefs file
- -w, --web_flag
- Web codebase jnlp flag [default: False]
- -u, --url
- Url path for the tep file. Note: when passing this flag, it will overwrite the supplied OTU table, Mapping and Tree files.
Output:
The result of this script is written to a .tep file and a .jnlp file, both with the name supplied by -o
Example:
Create .tep file and .jnlp file:
make_tep.py -i otu_table.biom -m Fasting_Map.txt -t rep_set.tre