--- a/env/lib/python3.7/site-packages/planemo/training/tool_input.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,231 +0,0 @@
-"""Module contains code for the ToolInput class, dealing with the description of tool in workflow and XML."""
-
-from planemo import templates
-from planemo.io import info
-
-
-INPUT_PARAM = """
->{{space}}- *"{{param_label}}"*: `{{param_value}}`
-"""
-
-INPUT_FILE_TEMPLATE = """
->{{space}}- {{ '{%' }} icon {{icon}} {{ '%}' }} *"{{input_name}}"*: {{input_value}}
-"""
-
-INPUT_SECTION = """
->{{space}}- In *"{{section_label}}"*:
-"""
-
-INPUT_ADD_REPEAT = """
->{{space}}- {{ '{%' }} icon param-repeat {{ '%}' }} *"Insert {{repeat_label}}"*
-"""
-
-SPACE = '    '
-
-
-class ToolInput(object):
-    """Class to describe a tool input / parameter and its value from a workflow."""
-
-    def __init__(self, tool_inp_desc, wf_param_values, wf_steps, level, should_be_there=False, force_default=False):
-        """Init an instance of ToolInput."""
-        self.name = tool_inp_desc['name']
-        if 'type' not in tool_inp_desc:
-            raise ValueError("No type for the parameter %s" % tool_inp_desc['name'])
-        self.type = tool_inp_desc['type']
-        self.tool_inp_desc = tool_inp_desc
-        self.level = level
-        self.wf_param_values = wf_param_values
-        self.wf_steps = wf_steps
-        self.formatted_desc = ''
-        self.force_default = force_default
-
-        if self.name not in self.wf_param_values:
-            if not should_be_there:
-                info("%s not in workflow" % self.name)
-            else:
-                raise ValueError("%s not in workflow" % (self.name))
-        else:
-            self.wf_param_values = self.wf_param_values[self.name]
-
-    def get_formatted_inputs(self):
-        """Format the inputs of a step."""
-        inputlist = ''
-        inps = []
-        if isinstance(self.wf_param_values, list):
-            # multiple input (not collection)
-            icon = 'param-files'
-            for i in self.wf_param_values:
-                inps.append('`%s` %s' % (
-                    i['output_name'],
-                    get_input_tool_name(i['id'], self.wf_steps)))
-        else:
-            inp = self.wf_param_values
-            if 'id' in inp:
-                # sinle input or collection
-                inp_type = self.wf_steps[str(inp['id'])]['type']
-                if 'collection' in inp_type:
-                    icon = 'param-collection'
-                else:
-                    icon = 'param-file'
-                inps = ['`%s` %s' % (
-                    inp['output_name'],
-                    get_input_tool_name(inp['id'], self.wf_steps))]
-        if len(inps) > 0:
-            inputlist += templates.render(INPUT_FILE_TEMPLATE, **{
-                "icon": icon,
-                "input_name": self.tool_inp_desc['label'],
-                "input_value": ', '.join(inps),
-                "space": SPACE * self.level
-            })
-        return inputlist
-
-    def get_lower_param_desc(self):
-        """Get the formatted description of the paramaters in the 'inputs' of the tool description."""
-        sub_param_desc = ''
-        for inp in self.tool_inp_desc["inputs"]:
-            tool_inp = ToolInput(
-                inp,
-                self.wf_param_values,
-                self.wf_steps,
-                self.level + 1)
-            sub_param_desc += tool_inp.get_formatted_desc()
-        return sub_param_desc
-
-    def get_formatted_section_desc(self):
-        """Format the description (label and value) for parameters in a section."""
-        section_paramlist = ''
-        sub_param_desc = self.get_lower_param_desc()
-        if sub_param_desc != '':
-            section_paramlist += templates.render(INPUT_SECTION, **{
-                'space': SPACE * self.level,
-                'section_label': self.tool_inp_desc['title']})
-            section_paramlist += sub_param_desc
-        return section_paramlist
-
-    def get_formatted_conditional_desc(self):
-        """Format the description (label and value) for parameters in a conditional."""
-        conditional_paramlist = ''
-        # Get conditional parameter
-        inp = ToolInput(
-            self.tool_inp_desc['test_param'],
-            self.wf_param_values,
-            self.wf_steps,
-            self.level,
-            should_be_there=True,
-            force_default=True)
-        conditional_paramlist = inp.get_formatted_desc()
-        cond_param = inp.wf_param_values
-
-        # Get parameters in the when and their values
-        tmp_tool_inp_desc = self.tool_inp_desc
-        for case in tmp_tool_inp_desc['cases']:
-            if case['value'] == cond_param and len(case['inputs']) > 0:
-                self.tool_inp_desc = case
-                conditional_paramlist += self.get_lower_param_desc()
-        self.tool_inp_desc = tmp_tool_inp_desc
-        return conditional_paramlist
-
-    def get_formatted_repeat_desc(self):
-        """Format the description (label and value) for parameters in a repeat."""
-        repeat_paramlist = ''
-        if self.wf_param_values != '[]':
-            tool_inp = {}
-            for inp in self.tool_inp_desc["inputs"]:
-                tool_inp.setdefault(inp['name'], inp)
-            tmp_wf_param_values = self.wf_param_values
-            cur_level = self.level
-            for ind, param in enumerate(tmp_wf_param_values):
-                self.wf_param_values = param
-                self.level = cur_level + 1
-                paramlist_in_repeat = self.get_lower_param_desc()
-                if paramlist_in_repeat != '':
-                    # add first click
-                    repeat_paramlist += templates.render(INPUT_ADD_REPEAT, **{
-                        'space': SPACE * (self.level),
-                        'repeat_label': self.tool_inp_desc['title']})
-                    repeat_paramlist += paramlist_in_repeat
-                self.level = cur_level
-            self.wf_param_values = tmp_wf_param_values
-
-        repeat_desc = ''
-        if repeat_paramlist != '':
-            repeat_desc += templates.render(INPUT_SECTION, **{
-                'space': SPACE * self.level,
-                'section_label': self.tool_inp_desc['title']}) + repeat_paramlist
-        return repeat_desc
-
-    def get_formatted_other_param_desc(self):
-        """Get value of a 'simple' parameter if different from the default value, None otherwise."""
-        param_value = None
-        if self.tool_inp_desc['value'] == self.wf_param_values and not self.force_default:
-            param_value = None
-        elif self.type == 'boolean':
-            if bool(self.tool_inp_desc['value']) == self.wf_param_values:
-                param_value = None
-            else:
-                param_value = 'Yes' if self.wf_param_values else 'No'
-        elif self.type == 'select':
-            param_values = []
-            for opt in self.tool_inp_desc['options']:
-                if opt[1] == self.wf_param_values:
-                    param_values.append(opt[0])
-            param_value = ', '.join(param_values)
-        elif self.type == 'data_column':
-            param_value = "c%s" % self.wf_param_values
-        else:
-            param_value = self.wf_param_values
-
-        param_desc = ''
-        if param_value is not None:
-            param_desc = templates.render(INPUT_PARAM, **{
-                'space': SPACE * self.level,
-                'param_label': self.tool_inp_desc['label'],
-                'param_value': param_value})
-        return param_desc
-
-    def get_formatted_desc(self):
-        """Get the formatted description (ready for hands-on tutorial) of the parameter."""
-        if self.wf_param_values:
-            if self.type == 'data' or self.type == 'data_collection':
-                self.formatted_desc += self.get_formatted_inputs()
-            elif self.type == 'section':
-                self.formatted_desc += self.get_formatted_section_desc()
-            elif self.type == 'conditional':
-                self.formatted_desc += self.get_formatted_conditional_desc()
-            elif self.type == 'repeat':
-                self.formatted_desc += self.get_formatted_repeat_desc()
-            else:
-                self.formatted_desc += self.get_formatted_other_param_desc()
-        return self.formatted_desc
-
-
-def get_input_tool_name(step_id, steps):
-    """Get the string with the name of the tool that generated an input."""
-    inp_provenance = ''
-    inp_prov_id = str(step_id)
-    if inp_prov_id in steps:
-        name = steps[inp_prov_id]['name']
-        if 'Input dataset' in name:
-            inp_provenance = "(%s)" % name
-        else:
-            inp_provenance = "(output of **%s** {%% icon tool %%})" % name
-    return inp_provenance
-
-
-def get_empty_input():
-    """Get the string for an empty input."""
-    return templates.render(INPUT_FILE_TEMPLATE, **{
-        'space': 1 * SPACE,
-        'icon': 'param-file',
-        'input_name': 'Input file',
-        'input_value': 'File'
-    })
-
-
-def get_empty_param():
-    """Get the string for an empty param."""
-    return templates.render(INPUT_PARAM, **{
-        'space': 1 * SPACE,
-        'param_label': 'Parameter',
-        'param_value': 'a value'
-    })