+%endif
+
+ <%namespace file="/message.mako" import="render_msg" />
+ <%namespace file="/base_panels.mako" import="overlay" />
+
+ <% import galaxy.util %>
+
+ <%def name="stylesheets()">
+ ${h.css( "autocomplete_tagging", "base", "library" )}
+
+
+
+ <%def name="javascripts()">
+ ${parent.javascripts()}
+ ${h.js( "galaxy.panels", "libs/jquery/jstorage" )}
+ ${h.js( "libs/bibtex" )}
+
+
+
+
+
+ <%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
+ <%
+ from galaxy.util.expressions import ExpressionContext
+ other_values = ExpressionContext( tool_state, other_values )
+ %>
+ %for input_index, input in enumerate( inputs.itervalues() ):
+ %if not input.visible:
+ <% pass %>
+ %elif input.type == "repeat":
+
+ %endif + + <% + # Render an error message if a dynamically generated select list is missing a required + # index file or entry in the tool_data_table_conf.xml file. + message = "" + params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry + params_with_missing_index_file = tool.params_with_missing_index_file + if params_with_missing_data_table_entry: + param = params_with_missing_data_table_entry[0] + message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name + if tool.params_with_missing_index_file: + param = params_with_missing_index_file[0] + message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file + + # Handle calculating the redirect url for the special case where we have nginx proxy + # upload and need to do url_for on the redirect portion of the tool action. + try: + tool_url = h.url_for(tool.action) + except AttributeError: + assert len(tool.action) == 2 + tool_url = tool.action[0] + h.url_for(tool.action[1]) + %> + + <% + # Name of the tool in lower case + low_tool_name = tool.name.lower() + %> + + %if tool_id_version_message: + ${render_msg( tool_id_version_message, 'warning' )} + %endif + +
+ })
${rep_errors['__index__']}
+ %endif
+ %endfor
+ %if input.max > num_repeats:
+
+ %endif
+
+ %elif input.type == "conditional":
+ <%
+ group_state = tool_state[input.name]
+ group_errors = errors.get( input.name, {} )
+ current_case = group_state['__current_case__']
+ group_prefix = prefix + input.name + "|"
+ %>
+ %if input.value_ref_in_group:
+ ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
+ %endif
+ ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
+ %elif input.type == "upload_dataset":
+ %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before
+ <%
+ if input.name in errors:
+ rep_errors = errors[input.name][0]
+ else:
+ rep_errors = dict()
+ %>
+ ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )}
+ %else:
+ ${input.title_plural}
+ %if input.help:
+
+ <%
+ repeat_state = tool_state[input.name]
+ num_repeats = len( repeat_state )
+ %>
+ %for i in range( num_repeats ):
+
+ ${input.help}
+
+ %endif
+
+ <%
+ if input.name in errors:
+ rep_errors = errors[input.name][i]
+ else:
+ rep_errors = dict()
+ index = repeat_state[i]['__index__']
+ %>
+
+ %if rep_errors.has_key( '__index__' ):
+ ${input.title} ${i + 1}
+ ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
+ %if input.min < num_repeats:
+
+ %endif
+ ${rep_errors['__index__']}
+
+ %endif
+ %elif input.type != "section":
+ ${row_for_param( prefix, input, tool_state, errors, other_values )}
+ %endif
+ %endfor
+
+
+ <%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
+ <%
+ if parent_errors.has_key( param.name ):
+ cls = "form-row form-row-error"
+ else:
+ cls = "form-row"
+
+ field = param.get_html_field( trans, parent_state[ param.name ], other_values )
+ field.refresh_on_change = param.refresh_on_change
+
+ # Field may contain characters submitted by user and these characters may
+ # be unicode; handle non-ascii characters gracefully.
+ field_html = field.get_html( prefix )
+ if type( field_html ) is not unicode:
+ field_html = unicode( field_html, 'utf-8', 'replace' )
+
+ if param.type == "hidden":
+ return field_html
+ %>
+ ${input.group_title( other_values )}
+ <%
+ repeat_state = tool_state[input.name]
+ %>
+ %for i in range( len( repeat_state ) ):
+
+ <%
+ if input.name in errors:
+ rep_errors = errors[input.name][i]
+ else:
+ rep_errors = dict()
+ index = repeat_state[i]['__index__']
+ %>
+
+ %endfor
+ ##
+ File Contents for ${input.title_by_index( trans, i, other_values )}
+ ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
+ ##
+
+ ${label_for_param( param )}
+ ${input_for_param( param, field_html )}
+ ${errors_for_param( param, parent_errors )}
+ ${help_for_param( param )}
+
+
+
+
+ <%def name="input_for_param( param, field_html )">
+ ${field_html}
+
+
+ <%def name="label_for_param( param )">
+ <% label = param.get_label()%>
+ %if label:
+
+ %endif
+
+
+ <%def name="errors_for_param( param, parent_errors )">
+ %if parent_errors.has_key( param.name ):
+
+ ${parent_errors[param.name]}
+
+ %endif
+
+
+ <%def name="help_for_param( param )">
+ %if param.help:
+ ${parent_errors[param.name]}
+ ${param.help}
+
+ %endif
+
+
+ <%def name="row_for_rerun()">
+ %if trans.app.config.track_jobs_in_database and tool_state.rerun_remap_job_id is not None:
+
+ Resume dependencies from this job
+
+
+ %endif
+
+
+ <% overlay(visible=False) %>
+
+ %if add_frame.from_noframe:
+
+
+ The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run.
+
+ + %endif + + <% + # Render an error message if a dynamically generated select list is missing a required + # index file or entry in the tool_data_table_conf.xml file. + message = "" + params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry + params_with_missing_index_file = tool.params_with_missing_index_file + if params_with_missing_data_table_entry: + param = params_with_missing_data_table_entry[0] + message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name + if tool.params_with_missing_index_file: + param = params_with_missing_index_file[0] + message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file + + # Handle calculating the redirect url for the special case where we have nginx proxy + # upload and need to do url_for on the redirect portion of the tool action. + try: + tool_url = h.url_for(tool.action) + except AttributeError: + assert len(tool.action) == 2 + tool_url = tool.action[0] + h.url_for(tool.action[1]) + %> + + <% + # Name of the tool in lower case + low_tool_name = tool.name.lower() + %> + + %if tool_id_version_message: + ${render_msg( tool_id_version_message, 'warning' )} + %endif + +
+