Mercurial > repos > iuc > data_manager_omamer

changeset 1:57db282ca204 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
author iuc
date Thu, 07 Mar 2024 14:28:42 +0000
parents e1502e4f8725
children
files data_manager/macros.xml data_manager/omamer.py data_manager/omamer.xml data_manager/test.json data_manager_conf.xml test-data/omamer.loc test-data/out.json tool_data_table_conf.xml.test
diffstat 8 files changed, 40 insertions(+), 52 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/macros.xml	Wed Feb 21 19:26:53 2024 +0000
+++ b/data_manager/macros.xml	Thu Mar 07 14:28:42 2024 +0000
@@ -1,8 +1,12 @@
+
 <macros>
+    <token name="@TOOL_VERSION@">2.0.2</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="3.11">python</requirement>
             <requirement type="package" version="2.27.1">requests</requirement>
         </requirements>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
--- a/data_manager/omamer.py	Wed Feb 21 19:26:53 2024 +0000
+++ b/data_manager/omamer.py	Thu Mar 07 14:28:42 2024 +0000
@@ -4,7 +4,6 @@
 import json
 import os
 import sys
-from pathlib import Path
 
 import requests
 
@@ -19,7 +18,6 @@
     "LUCA": "LUCA-v0.2.5.h5",
 }
 
-
 DEFAULT_OUTPUT_DIR = "database_omamer"
 
 
@@ -37,12 +35,14 @@
 
 
 def main(args):
-    # Set output directory to default
-    output_dir = DEFAULT_OUTPUT_DIR
+
+    with open(args.json) as fh:
+        params = json.load(fh)
+    target_directory = params["output_data"][0]["extra_files_path"]
 
     # Create output directory if none exists
-    if not os.path.exists(output_dir):
-        os.makedirs(output_dir)
+    if not os.path.exists(target_directory):
+        os.makedirs(target_directory)
 
     # Check if the selected dataset exists
     if args.name not in OMAMER_DATASETS:
@@ -53,18 +53,18 @@
     dataset = OMAMER_DATASETS[args.name]
     url = OMAMER_DATASETS_URL.format(dataset=dataset)
     base_name = os.path.splitext(dataset)[0]
-    destination_path = os.path.join(output_dir, base_name)
+    destination_path = os.path.join(target_directory, dataset)
     download_file(url, destination_path)
 
     data_manager_entry = {
-        "value": os.path.splitext(os.path.basename(base_name))[0],
-        "name": os.path.splitext(os.path.basename(base_name))[0],
-        "version": "2.0.2",
-        "path": str(Path(output_dir)),
+        "value": dataset,
+        "name": base_name,
+        "version": args.version,
+        "path": dataset,
     }
 
     # Creates a JSON dictionary representing the Data Manager configuration
-    data_manager_json = {"data_tables": {"omamer_data": [data_manager_entry]}}
+    data_manager_json = {"data_tables": {"omamer": [data_manager_entry]}}
 
     # Writes this JSON dictionary to the specified output file
     with open(args.json, "w") as fh:
@@ -76,6 +76,7 @@
     parser = argparse.ArgumentParser(description='Download data for OMAmer')
     parser.add_argument('--name', default='Primates', choices=OMAMER_DATASETS.keys(), help='Select dataset to download')
     parser.add_argument('--json', help='Path to JSON file')
+    parser.add_argument("--version", help="Omamer version")
 
     args = parser.parse_args()
 
--- a/data_manager/omamer.xml	Wed Feb 21 19:26:53 2024 +0000
+++ b/data_manager/omamer.xml	Thu Mar 07 14:28:42 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="data_manager_omamer" name="OMAmer data manager" version="2.0.2" tool_type="manage_data" profile="20.01">
+<tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -7,6 +7,7 @@
         python '$__tool_directory__/omamer.py'
         --name '$name'
         --json '$output_file'
+        --version '@TOOL_VERSION@'
     ]]></command>
     <inputs>
         <param name="output_dir" type="text" label="Output Directory" value=""/>
@@ -17,7 +18,7 @@
             <option value="LUCA">LUCA</option>
         </param>
     </inputs>
-    
+
     <outputs>
         <data name="output_file" format="data_manager_json" label="OMAmer data manager: JSON"/>
     </outputs>
@@ -26,15 +27,10 @@
         <test>
             <param name="output_dir" value="test_galaxy"/>
             <param name="name" value="Primates"/>
-            <output name="output_file">
-                <assert_contents>
-                    <has_text text="Primates-v2.0"/>
-                    <has_text text="database_omamer"/>
-                </assert_contents>
-            </output>
+            <output name="output_file" file="out.json"/>
         </test>
     </tests>
-    
+
     <help><![CDATA[
         This data manager retrieves data from various pre-built databases.
 
@@ -43,4 +39,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btab219</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
--- a/data_manager/test.json	Wed Feb 21 19:26:53 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-{
-  "data_tables": {
-    "omamer_data": [
-      {
-        "name": "Primates-v2.0",
-        "path": "database_omamer",
-        "value": "Primates-v2.0",
-        "version": "2.0.2"
-      }
-    ]
-  }
-}
\ No newline at end of file
--- a/data_manager_conf.xml	Wed Feb 21 19:26:53 2024 +0000
+++ b/data_manager_conf.xml	Thu Mar 07 14:28:42 2024 +0000
@@ -6,8 +6,9 @@
                 <column name="value" />
                 <column name="name" />
                 <column name="version"/>
-                <column name="path" output_ref="out_file">
-                    <move type="directory" relativize_symlinks="True">
+                <column name="path" output_ref="output_file">
+                    <move type="file">
+                        <source>${path}</source>
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">omamer/${value}</target>
                     </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/omamer/${value}</value_translation>
@@ -16,4 +17,4 @@
             </output>
         </data_table>
     </data_manager>
-</data_managers>
\ No newline at end of file
+</data_managers>
--- a/test-data/omamer.loc	Wed Feb 21 19:26:53 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-# this is a tab separated file describing the location of OMAmer databases used for the
-# OMAmer annotation tool
-#
-# the columns are:
-# value name version path
-#
-# for example
-# Primates-v2.0.0	Primates	2.0.2	/tmp/database/omamer/database_omamer/Primates-v2.0.0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.json	Thu Mar 07 14:28:42 2024 +0000
@@ -0,0 +1,12 @@
+{
+  "data_tables": {
+    "omamer": [
+      {
+        "name": "Primates-v2.0.0",
+        "path": "Primates-v2.0.0.h5",
+        "value": "Primates-v2.0.0.h5",
+        "version": "2.0.2"
+      }
+    ]
+  }
+}
\ No newline at end of file
--- a/tool_data_table_conf.xml.test	Wed Feb 21 19:26:53 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="omamer" comment_char="#">
-        <columns>value, name, version, path</columns>
-        <file path="${__HERE__}/test-data/omamer.loc"/>
-    </table>
-</tables>
\ No newline at end of file