Merge pull request #11711 from mvdbeek/dev

Merge 20.09 into dev
2026-10-24 02:04:04 +08:00 · 2021-03-25 16:37:05 +01:00
parent 312731dfeb c9d63b9029
commit a4440f4002
25 changed files with 235 additions and 116 deletions
@@ -9,7 +9,8 @@ import LIST_CREATOR from "components/Collections/ListCollectionCreator";
 import LIST_CREATOR_MODAL from "components/Collections/ListCollectionCreatorModal";
 import PAIR_CREATOR from "components/Collections/PairCollectionCreator";
 import PAIR_CREATOR_MODAL from "components/Collections/PairCollectionCreatorModal";
-import PAIRED_CREATOR from "components/Collections/PairedListCollectionCreatorModal";
+import PAIRED_CREATOR from "components/Collections/PairedListCollectionCreator";
+import PAIRED_CREATOR_MODAL from "components/Collections/PairedListCollectionCreatorModal";
 import RULE_CREATOR_MODAL from "components/Collections/RuleBasedCollectionCreatorModal";
 import HDCA_MODEL from "mvc/history/hdca-model";

@@ -33,8 +34,10 @@ var ImportCollectionModal = Backbone.View.extend({
        this.histories = new mod_library_model.GalaxyHistories();
        return this.histories.fetch();
    },
-    createNewHistory: function (new_history_name) {
-        return axios.post(`${getAppRoot()}api/histories`, { name: new_history_name });
+    async createNewHistory(new_history_name) {
+        const { data } = await axios.post(`${getAppRoot()}api/histories`, { name: new_history_name });
+        getGalaxyInstance().currHistoryPanel.switchToHistory(data.id);
+        return data;
    },
    showCollectionSelect: function (e) {
        const Galaxy = getGalaxyInstance();
@@ -144,16 +147,32 @@ var ImportCollectionModal = Backbone.View.extend({
                creator_class
            );
        } else if (this.collectionType === "list:paired") {
-            const elements = collection_elements.map((element) => ({
-                id: element.id,
-                name: element.name,
-                src: "ldda",
-            }));
-            PAIRED_CREATOR.pairedListCollectionCreatorModal(elements, {
-                historyId: history_id,
-                title: modal_title,
-                defaultHideSourceItems: true,
-            });
+            creator_class = PAIRED_CREATOR;
+            creationFn = (elements, name, hideSourceItems) => {
+                elements = elements.map((pair) => ({
+                    collection_type: "paired",
+                    src: "new_collection",
+                    name: pair.name,
+                    element_identifiers: [
+                        {
+                            name: "forward",
+                            id: pair.forward.id,
+                            src: "ldda",
+                        },
+                        {
+                            name: "reverse",
+                            id: pair.reverse.id,
+                            src: "ldda",
+                        },
+                    ],
+                }));
+                return this.createHDCA(elements, "list:paired", name, hideSourceItems, history_id);
+            };
+            PAIRED_CREATOR_MODAL.pairedListCollectionCreatorModal(
+                collection_elements,
+                { creationFn: creationFn, title: modal_title, defaultHideSourceItems: true },
+                creator_class
+            );
        } else if (this.collectionType === "rules") {
            const creationFn = (elements, collectionType, name, hideSourceItems) => {
                return this.createHDCA(elements, collectionType, name, hideSourceItems, history_id);
@@ -35,7 +35,9 @@
        @show="open(tab, $event)"
    >
        <template v-for="(item, idx) in tab.menu">
+            <div v-if="item.divider" class="dropdown-divider" :key="`divider-${idx}`" />
            <b-dropdown-item
+                v-else-if="item.hidden !== true"
                :href="formatUrl(item.url)"
                :key="`item-${idx}`"
                :target="item.target || '_parent'"
@@ -45,7 +47,6 @@
            >
                {{ item.title }}
            </b-dropdown-item>
-            <div v-if="item.divider" class="dropdown-divider" :key="`divider-${idx}`" />
        </template>
    </b-nav-item-dropdown>
 </template>
@@ -32,41 +32,43 @@
                </div>
            </div>
        </b-row>
-        <b-row class="ml-3 mb-1">
-            <i class="pref-icon pt-1 fa fa-lg fa-radiation" />
-            <div class="pref-content pr-1">
-                <a href="javascript:void(0)"><b v-b-modal.modal-prevent-closing>Delete Account</b></a>
-                <div class="form-text text-muted">Delete your account on this Galaxy server.</div>
-                <b-modal
-                    id="modal-prevent-closing"
-                    centered
-                    ref="modal"
-                    title="Account Deletion"
-                    title-tag="h2"
-                    @show="resetModal"
-                    @hidden="resetModal"
-                    @ok="handleOk"
-                >
-                    <p>
-                        <b-alert variant="danger" :show="showDeleteError">{{ deleteError }}</b-alert>
-                        <b>
-                            This action cannot be undone. Your account will be permanently deleted, along with the data
-                            contained in it.
-                        </b>
-                    </p>
-                    <b-form ref="form" @submit.prevent="handleSubmit">
-                        <b-form-group
-                            :state="nameState"
-                            label="Enter your user email for this account as confirmation."
-                            label-for="Email"
-                            invalid-feedback="Incorrect email"
-                        >
-                            <b-form-input id="name-input" v-model="name" :state="nameState" required></b-form-input>
-                        </b-form-group>
-                    </b-form>
-                </b-modal>
-            </div>
-        </b-row>
+        <ConfigProvider v-slot="{ config }">
+            <b-row v-if="config && !config.single_user" class="ml-3 mb-1">
+                <i class="pref-icon pt-1 fa fa-lg fa-radiation" />
+                <div class="pref-content pr-1">
+                    <a href="javascript:void(0)"><b v-b-modal.modal-prevent-closing>Delete Account</b></a>
+                    <div class="form-text text-muted">Delete your account on this Galaxy server.</div>
+                    <b-modal
+                        id="modal-prevent-closing"
+                        centered
+                        ref="modal"
+                        title="Account Deletion"
+                        title-tag="h2"
+                        @show="resetModal"
+                        @hidden="resetModal"
+                        @ok="handleOk"
+                    >
+                        <p>
+                            <b-alert variant="danger" :show="showDeleteError">{{ deleteError }}</b-alert>
+                            <b>
+                                This action cannot be undone. Your account will be permanently deleted, along with the
+                                data contained in it.
+                            </b>
+                        </p>
+                        <b-form ref="form" @submit.prevent="handleSubmit">
+                            <b-form-group
+                                :state="nameState"
+                                label="Enter your user email for this account as confirmation."
+                                label-for="Email"
+                                invalid-feedback="Incorrect email"
+                            >
+                                <b-form-input id="name-input" v-model="name" :state="nameState" required></b-form-input>
+                            </b-form-group>
+                        </b-form>
+                    </b-modal>
+                </div>
+            </b-row>
+        </ConfigProvider>
        <p class="mt-2">
            You are using <strong>{{ diskUsage }}</strong> of disk space in this Galaxy instance.
            <span v-html="quotaUsageString"></span>
@@ -86,6 +88,7 @@ import _l from "utils/localization";
 import axios from "axios";
 import QueryStringParsing from "utils/query-string-parsing";
 import { getUserPreferencesModel } from "components/User/UserPreferencesModel";
+import ConfigProvider from "components/providers/ConfigProvider";
 import { userLogoutAll, userLogoutClient } from "layout/menu";
 import "@fortawesome/fontawesome-svg-core";

@@ -102,6 +105,9 @@ export default {
            required: true,
        },
    },
+    components: {
+        ConfigProvider,
+    },
    data() {
        return {
            email: "",
@@ -42,12 +42,14 @@ export const getUserPreferencesModel = () => {
            icon: "fa-users",
            submit_title: "Save Permissions",
            redirect: "user",
+            shouldRender: !config.single_user,
        },
        make_data_private: {
            title: _l("Make All Data Private"),
            id: "edit-preferences-make-data-private",
            description: _l("Click here to make all data private."),
            icon: "fa-lock",
+            shouldRender: !config.single_user,
        },
        api_key: {
            title: _l("Manage API Key"),
@@ -86,7 +88,7 @@ export const getUserPreferencesModel = () => {
            id: "edit-preferences-sign-out",
            description: _l("Click here to sign out of all sessions."),
            icon: "fa-sign-out",
-            shouldRender: !!Galaxy.session_csrf_token,
+            shouldRender: !!Galaxy.session_csrf_token && !config.single_user,
        },
    };
 };
@@ -243,15 +243,19 @@ export default {
        },
        onAddInput(input, terminal) {
            this.inputTerminals[input.name] = terminal;
+            this.onRedraw();
        },
        onRemoveInput(input) {
            delete this.inputTerminals[input.name];
+            this.onRedraw();
        },
        onAddOutput(output, terminal) {
            this.outputTerminals[output.name] = terminal;
+            this.onRedraw();
        },
        onRemoveOutput(output) {
            delete this.outputTerminals[output.name];
+            this.onRedraw();
        },
        onToggleOutput(name) {
            this.activeOutputs.toggle(name);
@@ -114,38 +114,49 @@ export function fetchMenu(options = {}) {
    //
    // 'Shared Items' or Libraries tab.
    //
-    menu.push({
-        id: "shared",
-        title: _l("Shared Data"),
-        url: "javascript:void(0)",
-        tooltip: _l("Access published resources"),
-        menu: [
-            {
-                title: _l("Data Libraries"),
-                url: "libraries",
-            },
-            {
-                title: _l("Histories"),
-                url: "histories/list_published",
-                target: "__use_router__",
-            },
-            {
-                title: _l("Workflows"),
-                url: "workflows/list_published",
-                target: "__use_router__",
-            },
-            {
-                title: _l("Visualizations"),
-                url: "visualizations/list_published",
-                target: "__use_router__",
-            },
-            {
-                title: _l("Pages"),
-                url: "pages/list_published",
-                target: "__use_router__",
-            },
-        ],
-    });
+    if (Galaxy.config.single_user) {
+        // Single user can still use libraries, especially as we may grow that
+        // functionality as a representation for external data.  The rest is
+        // hidden though.
+        menu.push({
+            title: _l("Data Libraries"),
+            url: "libraries",
+            id: "libraries",
+        });
+    } else {
+        menu.push({
+            id: "shared",
+            title: _l("Shared Data"),
+            url: "javascript:void(0)",
+            tooltip: _l("Access published resources"),
+            menu: [
+                {
+                    title: _l("Data Libraries"),
+                    url: "libraries",
+                },
+                {
+                    title: _l("Histories"),
+                    url: "histories/list_published",
+                    target: "__use_router__",
+                },
+                {
+                    title: _l("Workflows"),
+                    url: "workflows/list_published",
+                    target: "__use_router__",
+                },
+                {
+                    title: _l("Visualizations"),
+                    url: "visualizations/list_published",
+                    target: "__use_router__",
+                },
+                {
+                    title: _l("Pages"),
+                    url: "pages/list_published",
+                    target: "__use_router__",
+                },
+            ],
+        });
+    }

    //
    // Admin.
@@ -271,10 +282,11 @@ export function fetchMenu(options = {}) {
                    url: "custom_builds",
                    target: "__use_router__",
                },
+                { divider: true },
                {
                    title: _l("Logout"),
-                    divider: true,
                    onclick: userLogout,
+                    hidden: Galaxy.config.single_user,
                },
                {
                    title: _l("Datasets"),
@@ -290,6 +302,7 @@ export function fetchMenu(options = {}) {
                    title: _l("Histories shared with me"),
                    url: "histories/list_shared",
                    target: "__use_router__",
+                    hidden: Galaxy.config.single_user,
                },
                {
                    title: _l("Pages"),
@@ -311,7 +324,7 @@ export function fetchMenu(options = {}) {
            });
        }
        if (Galaxy.config.interactivetools_enable) {
-            userTab.menu[userTab.menu.length - 1].divider = true;
+            userTab.menu.push({ divider: true });
            userTab.menu.push({
                title: _l("Active InteractiveTools"),
                url: "interactivetool_entry_points/list",
@@ -320,6 +333,5 @@ export function fetchMenu(options = {}) {
        }
    }
    menu.push(userTab);
-
    return menu;
 }
@@ -140,7 +140,10 @@ export default Backbone.Model.extend({
    /** Text input field */
    _fieldText: function (input_def) {
        // field replaces e.g. a select field
-        if (input_def.model_class === "SelectTagParameter" || (input_def.options && input_def.data)) {
+        if (
+            ["SelectTagParameter", "ColumnListParameter"].includes(input_def.model_class) ||
+            (input_def.options && input_def.data)
+        ) {
            input_def.area = input_def.multiple;
            if (Utils.isEmpty(input_def.value)) {
                input_def.value = null;
@@ -32,6 +32,7 @@ var menu = [
                Galaxy.router.push(`/histories/sharing?id=${Galaxy.currHistoryPanel.model.id}`);
            }
        },
+        singleUserDisable: true,
    },
    {
        html: _l("Show Structure"),
@@ -55,6 +56,7 @@ var menu = [
                Galaxy.router.push(`/histories/permissions?id=${Galaxy.currHistoryPanel.model.id}`);
            }
        },
+        singleUserDisable: true,
    },
    {
        html: _l("Make Private"),
@@ -200,7 +202,11 @@ Webhooks.load({
 });

 function buildMenu(isAnon, purgeAllowed, urlRoot) {
+    const Galaxy = getGalaxyInstance();
    return _.clone(menu).filter((menuOption) => {
+        if (Galaxy.config.single_user && menuOption.singleUserDisable) {
+            return false;
+        }
        if (isAnon && !menuOption.anon) {
            return false;
        }
@@ -357,6 +357,19 @@ var View = Backbone.View.extend({
                            (!input_def.is_workflow && input_value !== null);
                    }
                    if (!validated) {
+                        if (input_def.type == "hidden") {
+                            this.modal.show({
+                                title: _l("Workflow submission failed"),
+                                body: `Step ${step_index}: ${
+                                    step.step_label || step.step_name
+                                } is in an invalid state. Please remove and re-add this step in the Workflow Editor.`,
+                                buttons: {
+                                    Close: () => {
+                                        this.modal.hide();
+                                    },
+                                },
+                            });
+                        }
                        form.highlight(input_id);
                        break;
                    }
@@ -197,6 +197,7 @@
    <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
    <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
    <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
+    <datatype extension="hhr" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
    <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
    <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff" display_in_upload="true"/>
    <datatype extension="tf2" type="galaxy.datatypes.images:Tiff" subclass="true" display_in_upload="false"/>
@@ -265,6 +266,7 @@
    <datatype extension="mztab2" type="galaxy.datatypes.proteomics:MzTab2" display_in_upload="true"/>
    <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
    <datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
+    <datatype extension="meryldb" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" description="MerylDB is a tar.gz archive containing 64 binaries + 64 indexes."/>
    <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
    <datatype extension="wiff" type="galaxy.datatypes.proteomics:Wiff" display_in_upload="true"/>
    <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml" display_in_upload="true"/>
@@ -1348,7 +1348,10 @@ class JobWrapper(HasResourceParameters):
            ActionBox.execute(self.app, self.sa_session, pja, job)
        # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
        if self.tool:
-            self.tool.job_failed(self, message, exception)
+            try:
+                self.tool.job_failed(self, message, exception)
+            except Exception:
+                log.exception(f"Error occured while calling tool specific fail actions for job {job.id}")
        cleanup_job = self.cleanup_job
        delete_files = cleanup_job == 'always' or (cleanup_job == 'onsuccess' and job.state == job.states.DELETED)
        self.cleanup(delete_files=delete_files)
@@ -141,7 +141,9 @@ class BaseJobRunner:
                    job_state = JobState(job_wrapper=arg, job_destination={})
                else:
                    job_state = arg
-                self.work_queue.put((self.fail_job, job_state))
+                if method != self.fail_job:
+                    # Prevent fail_job cycle in the work_queue
+                    self.work_queue.put((self.fail_job, job_state))

    # Causes a runner's `queue_job` method to be called from a worker thread
    def put(self, job_wrapper):
@@ -122,6 +122,9 @@ class ConfigSerializer(base.ModelSerializer):
            assert hasattr(config, key)
            return getattr(config, key)

+        def _config_is_truthy(config, key, **context):
+            return True if config.get(key) else False
+
        self.serializers = {
            # TODO: this is available from user data, remove
            'is_admin_user': lambda *a, **c: False,
@@ -151,6 +154,7 @@ class ConfigSerializer(base.ModelSerializer):
            'allow_user_impersonation': _use_config,
            'allow_user_creation': _defaults_to(False),  # schema default is True
            'use_remote_user': _defaults_to(None),  # schema default is False; or config.single_user
+            'single_user': _config_is_truthy,
            'enable_oidc': _use_config,
            'oidc': _use_config,
            'enable_quotas': _use_config,
@@ -160,7 +164,6 @@ class ConfigSerializer(base.ModelSerializer):
            'ga_code': _use_config,
            'enable_unique_workflow_defaults': _use_config,
            'enable_beta_markdown_export': _use_config,
-            'simplified_workflow_run_ui': _use_config,
            'simplified_workflow_run_ui_target_history': _use_config,
            'simplified_workflow_run_ui_job_cache': _use_config,
            'has_user_tool_filters': _defaults_to(False),
@@ -401,7 +401,7 @@ class User(Dictifiable, RepresentById):
        extra_user_preferences = self.preferences.get('extra_user_preferences')
        if extra_user_preferences:
            try:
-                data = json.loads(extra_user_preferences)
+                data.update(json.loads(extra_user_preferences))
            except Exception:
                pass
        return data
@@ -361,6 +361,7 @@ tool_form:
    options: '#options [data-toggle="dropdown"]'
    execute: 'button#execute'
    parameter_div: 'div.ui-form-element[tour_id="${parameter}"]'
+    parameter_textarea: 'div.ui-form-element[tour_id="${parameter}"] textarea'
    reference: '.formatted-reference'
    about: '.tool-footer'

@@ -9,7 +9,14 @@ from boltons.iterutils import remap
 from galaxy.util import unicodify
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.json import safe_loads
-from .basic import DataCollectionToolParameter, DataToolParameter, is_runtime_value, runtime_to_json, SelectToolParameter
+from .basic import (
+    DataCollectionToolParameter,
+    DataToolParameter,
+    is_runtime_value,
+    ParameterValueError,
+    runtime_to_json,
+    SelectToolParameter,
+)
 from .grouping import Conditional, Repeat, Section, UploadDataset

 REPLACE_ON_TRUTHY = object()
@@ -229,7 +236,10 @@ def params_from_strings(params, param_values, app, ignore_errors=False):
            # This would resolve a lot of back and forth in the various to/from methods.
            value = safe_loads(value)
        if param:
-            value = param.value_from_basic(value, app, ignore_errors)
+            try:
+                value = param.value_from_basic(value, app, ignore_errors)
+            except ParameterValueError:
+                continue
        rval[key] = value
    return rval

@@ -212,6 +212,8 @@ class ToolParameter(Dictifiable):
    def value_from_basic(self, value, app, ignore_errors=False):
        # Handle Runtime and Unvalidated values
        if is_runtime_value(value):
+            if isinstance(self, HiddenToolParameter):
+                raise ParameterValueError(message_suffix='Runtime Parameter not valid', parameter_name=self.name)
            return runtime_to_object(value)
        elif isinstance(value, dict) and value.get('__class__') == 'UnvalidatedValue':
            return value['value']
@@ -137,6 +137,34 @@ class WorkflowEditorTestCase(SeleniumTestCase):
        self.sleep_for(self.wait_types.UX_RENDER)
        self.screenshot("workflow_editor_data_collection_input_deleted")

+    @selenium_test
+    def test_data_column_input_editing(self):
+        self.open_in_workflow_editor("""
+class: GalaxyWorkflow
+steps:
+  column_param_list:
+    tool_id: column_param_list
+    state:
+      col: ["1","2","3"]
+      col_names: ["a", "b", "c"]
+      """)
+        editor = self.components.workflow_editor
+        node = editor.node._(label="column_param_list")
+        node.title.wait_for_and_click()
+        columns = self.components.tool_form.parameter_textarea(parameter='col')
+        textarea_columns = columns.wait_for_visible()
+        assert textarea_columns.get_attribute('value') == '1\n2\n3\n'
+        column_names = self.components.tool_form.parameter_textarea(parameter='col_names')
+        textarea_column_names = column_names.wait_for_visible()
+        assert textarea_column_names.get_attribute('value') == 'a\nb\nc\n'
+        self.set_text_element(columns, '4\n5\n6\n')
+        self.assert_has_changes_and_save()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.driver.refresh()
+        node.title.wait_for_and_click()
+        textarea_columns = columns.wait_for_visible()
+        assert textarea_columns.get_attribute('value') == '4\n5\n6\n'
+
    @selenium_test
    def test_integer_input(self):
        editor = self.components.workflow_editor
@@ -6,11 +6,17 @@ History
 .. to_doc

 ---------------------
-20.5.1.dev0
+21.1.1.dev0
 ---------------------



+---------------------
+21.1.0 (2021-03-19)
+---------------------
+
+* First release from the 21.01 branch of Galaxy.
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
@@ -1,4 +1,4 @@
-__version__ = '20.5.1.dev0'
+__version__ = '21.1.1.dev0'

 PROJECT_NAME = "galaxy-containers"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
@@ -6,11 +6,17 @@ History
 .. to_doc

 ---------------------
-21.1.0.dev0
+21.1.1.dev0
 ---------------------



+---------------------
+21.1.0 (2021-03-19)
+---------------------
+
+* First release from the 21.01 branch of Galaxy.
+
 ---------------------
 20.9.1 (2020-10-28)
 ---------------------
@@ -1,4 +1,4 @@
-__version__ = '21.1.0.dev7'
+__version__ = '21.1.1.dev0'

 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
@@ -6,11 +6,17 @@ History
 .. to_doc

 ---------------------
-20.9.2.dev0
+21.1.1.dev0
 ---------------------



+---------------------
+21.1.0 (2021-03-19)
+---------------------
+
+* First release from the 21.01 branch of Galaxy.
+
 ---------------------
 20.9.1 (2020-10-28)
 ---------------------
@@ -1,4 +1,4 @@
-__version__ = '20.9.2.dev0'
+__version__ = '21.1.1.dev0'

 PROJECT_NAME = "galaxy-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
@@ -6,8 +6,8 @@ echo "col_names $col_names" >> '$output2'
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="tabular" label="Input 1" />
-        <param name="col" type="data_column" multiple="true" value="1" data_ref="input1" label="Column to Use" />
-        <param name="col_names" type="data_column" data_ref="input1" use_header_names="true" label="Column to Use" />
+        <param name="col" type="data_column" multiple="true" value="1" data_ref="input1" label="Columns to use" />
+        <param name="col_names" type="data_column" multiple="true" data_ref="input1" use_header_names="true" label="Column names to use" />
    </inputs>
    <outputs>
        <data name="output1" format="tabular" />
@@ -30,21 +30,5 @@ echo "col_names $col_names" >> '$output2'
                </assert_contents>
            </output>
        </test>
-        <!-- test if non tabular data also creates entries by using the default
-            value (which is the 1st column, but empty if filling the options fails) -->
-        <test>
-            <param name="input1" value="1.bed" />
-            <output name="output1">
-                <assert_contents>
-                    <has_line line="chr1" />
-                </assert_contents>
-            </output>
-            <output name="output2">
-                <assert_contents>
-                    <has_line line="col 1" />
-                    <has_line line="col_names 1" />
-                </assert_contents>
-            </output>
-        </test>
    </tests>
 </tool>