changeset 0:ef7f9e2f32f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/funannotate.py	Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import operator
+import os
+import subprocess
+import sys
+from datetime import datetime
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
+    parser.add_argument("version_id")
+    parser.add_argument("datatable_name")
+    parser.add_argument("galaxy_datamanager_filename")
+    args = parser.parse_args()
+
+    with open(args.galaxy_datamanager_filename) as fh:
+        config = json.load(fh)
+
+    output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
+    data_manager_dict = {}
+    data_manager_dict["data_tables"] = config.get("data_tables", {})
+    data_manager_dict["data_tables"][args.datatable_name] = data_manager_dict[
+        "data_tables"
+    ].get(args.datatable_name, [])
+
+    os.mkdir(output_directory)
+    cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all']
+    if args.partial:
+        cmd_args += ['-i', 'merops', '-b', 'eukaryota']
+    proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)
+    return_code = proc.wait()
+    if return_code:
+        print("Error downloading Funannotate database.", file=sys.stderr)
+        sys.exit(return_code)
+
+    version_id = datetime.today().strftime('%Y-%m-%d-%H%M%S')
+
+    version = '1.0'
+
+    data_manager_dict["data_tables"][args.datatable_name].append(
+        dict(
+            value=version_id,
+            description="Funannotate database %s" % version_id,
+            format_version=version,
+            path=output_directory,
+        )
+    )
+
+    data_manager_dict["data_tables"][args.datatable_name].sort(
+        key=operator.itemgetter("value"), reverse=True
+    )
+    with open(args.galaxy_datamanager_filename, "w") as fh:
+        json.dump(data_manager_dict, fh, indent=2, sort_keys=True)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/funannotate.xml	Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,39 @@
+<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.1" tool_type="manage_data" profile="20.01">
+    <requirements>
+        <requirement type="package" version="1.8.7">funannotate</requirement>
+    </requirements>
+    <version_command>funannotate check --show-versions</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/funannotate.py'
+$partial_data
+\$(date +'%Y-%m-%d-%H%M%S')
+'funannotate'
+'${output_file}'
+    ]]></command>
+    <inputs>
+        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="partial_data" value="--partial"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="Funannotate database "/>
+                    <has_text text='"format_version": "1.0"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This data managers fetches data from various databases for the funannotate
+        annotation tool and updates the funannotate data table.
+
+        .. _funannotate: https://funannotate.readthedocs.io
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.4054262</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/funannotate.xml" id="data_manager_funannotate">
+        <data_table name="funannotate">
+            <output>
+                <column name="value" />
+                <column name="description" />
+                <column name="format_version" />
+                <column name="path" output_ref="output_file" >
+                    <move type="directory" relativize_symlinks="True">
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">funannotate/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/funannotate/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/funannotate.loc	Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,9 @@
+# this is a tab separated file describing the location of funannotate databases used for the
+# funannotate annotation tool
+#
+# the columns are:
+# value  description format_version	path
+#
+# for example
+# 2021-07-20-120000	Funannotate database 2021-07-20-120000	1.0	/tmp/database/funannotate/2021-07-20-120000
+# 2021-05-27-120000	Funannotate database 2021-05-27-120000	3.0	/tmp/database/funannotate/2021-05-27-120000

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/funannotate.loc.sample	Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of funannotate databases used for the
+# funannotate annotation tool
+#
+# the columns are:
+# value  description format_version	path
+#
+# for example
+# 2021-07-20-120000	Funannotate database 2021-07-20-120000	1.0	/tmp/database/funannotate/funannotate/2021-07-20-120000

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="funannotate" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, description, format_version, path</columns>
+        <file path="tool-data/funannotate.loc" />
+    </table>
+</tables>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="funannotate" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, description, format_version, path</columns>
+        <file path="${__HERE__}/test-data/funannotate.loc" />
+    </table>
+</tables>