this works. general purpose interface factory functions are possible, and maybe even down to a single interface factory function. all the usage example, param conv, etc, can be described in an external file. what this means is that we describe commands as objects, but the interfaces are created dynamically.

dynamic CLI creation

#!/usr/bin/env python

from qcli.command import CLInterface, Command, \
        FilterSamplesFromOTUTable, CLOption

usage_examples = [("Abundance filtering (low coverage)","Filter samples with fewer than 150 observations from the otu table.","%prog -i otu_table.biom -o otu_table_no_low_coverage_samples.biom -n 150"),
                ("Abundance filtering (high coverage)","Filter samples with greater than 149 observations from the otu table.","%prog -i otu_table.biom -o otu_table_no_high_coverage_samples.biom -x 149"),
                ("Metadata-based filtering (positive)","Filter samples from the table, keeping samples where the value for 'Treatment' in the mapping file is 'Control'","%prog -i otu_table.biom -o otu_table_control_only.biom -m map.txt -s 'Treatment:Control'"),
                ("Metadata-based filtering (negative)","Filter samples from the table, keeping samples where the value for 'Treatment' in the mapping file is not 'Control'","%prog -i otu_table.biom -o otu_table_not_control.biom -m map.txt -s 'Treatment:*,!Control'"),
                ("List-based filtering","Filter samples where the id is listed in samples_to_keep.txt","%prog -i otu_table.biom -o otu_table_samples_to_keep.biom --sample_id_fp samples_to_keep.txt")]

param_conv = {'biom-table':{'short-name':'i',
                              'long-name':'input_fp',
                              'cl-type':'existing_filepath'},
                'min-count':{'short-name':'n',
                             'long-name':'min_count',
                             'cl-type':float},
                'max-count':{'short-name':'x',
                             'long-name':'max_count',
                             'cl-type':float}}

additional_opts = [CLOption(Type='biom-table',
                                        Help='the output otu table',
                                        Name='biom-table',
                                        Required=True,
                                        LongName='output_fp',
                                        CLType='new_filepath',
                                        ShortName='o')]

def cli_factory(cmd, usage_ex, p_conv, add_opts):
    class CLIobject(CLInterface):
        CommandConstructor = cmd
        def _get_param_conf_info(self):
            return p_conv
        def _get_additional_options(self):
            return add_opts
        def _get_usage_examples(self):
            return usage_ex
    return CLIobject

CLFilterSamplesFromOTUTable = cli_factory(FilterSamplesFromOTUTable, 
                                          usage_examples,
                                          param_conv, additional_opts)