changeset 0:b296fce41dd1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_artic_sars_cov2_primers.py	Fri Apr 17 12:10:23 2020 +0000
@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+
+from __future__ import print_function, division
+
+import argparse
+import json
+import os
+import os.path
+import sys
+
+import requests
+
+DATA_TABLE_NAME = 'artic_sars_cov2_primers'
+def fetch_artic_primers(output_filename, output_directory, primers):
+    primer_sets = {
+        'ARTICv1': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed',
+        'ARTICv2': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed',
+        'ARTICv3': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed'
+        }
+
+    if not os.path.isdir(output_directory):
+        os.makedirs(output_directory)
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = json.load(open(output_filename)).get('data_tables', {})
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables'][DATA_TABLE_NAME] = data_manager_dict['data_tables'].get(DATA_TABLE_NAME, [])
+    
+    data = []
+    for name, url in primer_sets.items():
+        if name not in primers:
+            continue
+        response = requests.get(url)
+        if response.status_code != 200:
+            print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr)
+            exit(response.status_code)
+        bed_output_filename = os.path.join(output_directory, name + '.bed')
+        open(bed_output_filename, 'w').write(response.text)
+        description = name[:-2] + ' ' + name[-2:] + ' primer set'
+        data.append(dict(value=name, path=bed_output_filename, description=description))
+    data_manager_dict['data_tables'][DATA_TABLE_NAME].extend(data)
+    print(data_manager_dict)
+    json.dump(data_manager_dict, open(output_filename, 'w'))
+
+class SplitArgs(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, values.split(','))
+
+                
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Fetch ARTIC SARS-CoV-2 primer files for Galaxy/IRIDA use')
+    parser.add_argument('--output_directory', default='tmp', help='Directory to write output to')
+    parser.add_argument('--galaxy_datamanager_filename', help='Galaxy JSON format file describing data manager inputs')
+    parser.add_argument('--primers', default='ARTICv1,ARTICv2,ARTICv3', action=SplitArgs, help='Comma separated list of primers to fetch')
+    args = parser.parse_args()
+    
+    config = json.load(open(args.galaxy_datamanager_filename))
+    output_directory = config.get('output_data', [{}])[0].get('extra_files_path', None)
+    if output_directory is None:
+        output_directory = args.output_directory
+    fetch_artic_primers(args.galaxy_datamanager_filename, output_directory, args.primers)
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_artic_sars_cov2_primers.xml	Fri Apr 17 12:10:23 2020 +0000
@@ -0,0 +1,32 @@
+<tool id="data_manager_fetch_artic_sars_cov2_primers" name="ARTIC SARS-CoV-2 primer data manager" version="0.0.5" tool_type="manage_data" profile="19.05">
+    <requirements>
+        <requirement type="package">python</requirement>
+        <requirement type="package" version="2.22.0">requests</requirement>
+    </requirements>
+    <!-- fetch all the primers in one go -->
+    <command detect_errors="exit_code">
+    python '$__tool_directory__/fetch_artic_sars_cov2_primers.py'
+        --galaxy_datamanager_filename '${output_file}'
+        --primers '${primers}'
+    </command>
+    <inputs>
+        <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch">
+            <option value="ARTICv1" selected="true">ARTIC v1</option>
+            <option value="ARTICv2" selected="true">ARTIC v2</option>
+            <option value="ARTICv3" selected="true">ARTIC v3</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="primers" value="ARTICv1,ARTICv2,ARTICv3"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="ARTIC"/>
+                </assert_contents>
+            </output>        
+        </test>
+    </tests>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Fri Apr 17 12:10:23 2020 +0000
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<data_managers>    
+    <data_manager tool_file="data_manager/fetch_artic_sars_cov2_primers.xml" id="fetch_artic_sars_cov2_primers">
+        <data_table name="artic_primers">
+            <output>
+                <column name="value" />
+                <column name="description" />
+                <column name="path" output_ref="output_file" >
+                    <move type="file">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">artic_sars_cov2_primers/#echo str($value)#.bed</target>
+                    </move>
+                    <value_translation>artic_sars_cov2_primers/#echo str($value)#.bed</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/tool-data/artic_sars_cov2_primers.loc.sample	Fri Apr 17 12:10:23 2020 +0000
@@ -0,0 +1,7 @@
+# this is a tab separated file describing the location of ARTIC primers for use in SARS-CoV-2 sequencing
+#
+# the columns are:
+# value  description path
+#
+# for example
+# ARTICv1   ARTIC v1 primers    /data/galaxy/tool_data/artic_primers/ARTICv1.bed
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Apr 17 12:10:23 2020 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all ARTIC SARS-CoV-2 primer BED files -->
+    <table name="artic_sars_cov2_primers" comment_char="#">
+        <columns>value, description, path</columns>
+        <file path="tool-data/artic_sars_cov2_primers.loc" />
+    </table>
+</tables>
\ No newline at end of file