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changeset 4:1c81a82b5b8e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
author iuc
date Fri, 07 Mar 2025 22:33:21 +0000
parents 0cadd0a04412
children 5459ec34767a
files data_manager/funannotate.py data_manager/funannotate.xml test-data/funannotate.loc
diffstat 3 files changed, 47 insertions(+), 302 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/funannotate.py	Fri Nov 19 15:43:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,286 +0,0 @@
-#!/usr/bin/env python
-
-import argparse
-import json
-import operator
-import os
-import subprocess
-import sys
-import tarfile
-from datetime import datetime
-
-import requests
-
-# Some additional busco/orthodb10 datasets that can be added to funannotate db
-# Will probably not be needed anymore in future versions of funannotate when it
-# will use a recent busco version
-BUSCO_10_DATASETS_URL = "https://busco-data.ezlab.org/v5/data/lineages/{dataset}"
-BUSCO_10_DATASETS = [
-    "acidobacteria_odb10.2020-03-06.tar.gz",
-    "aconoidasida_odb10.2020-08-05.tar.gz",
-    "actinobacteria_class_odb10.2021-02-23.tar.gz",
-    "actinobacteria_phylum_odb10.2021-02-23.tar.gz",
-    "actinopterygii_odb10.2021-02-19.tar.gz",
-    "agaricales_odb10.2020-08-05.tar.gz",
-    "agaricomycetes_odb10.2020-08-05.tar.gz",
-    "alphabaculovirus_odb10.2020-11-26.tar.gz",
-    "alphaherpesvirinae_odb10.2020-11-26.tar.gz",
-    "alphaproteobacteria_odb10.2021-02-23.tar.gz",
-    "alteromonadales_odb10.2021-02-23.tar.gz",
-    "alveolata_odb10.2020-09-10.tar.gz",
-    "apicomplexa_odb10.2020-09-10.tar.gz",
-    "aquificae_odb10.2021-02-23.tar.gz",
-    "arachnida_odb10.2020-08-05.tar.gz",
-    "archaea_odb10.2021-02-23.tar.gz",
-    "arthropoda_odb10.2020-09-10.tar.gz",
-    "ascomycota_odb10.2020-09-10.tar.gz",
-    "aves_odb10.2021-02-19.tar.gz",
-    "aviadenovirus_odb10.2020-11-26.tar.gz",
-    "bacillales_odb10.2021-02-23.tar.gz",
-    "bacilli_odb10.2021-02-23.tar.gz",
-    "bacteria_odb10.2020-03-06.tar.gz",
-    "bacteroidales_odb10.2021-02-23.tar.gz",
-    "bacteroidetes-chlorobi_group_odb10.2021-02-23.tar.gz",
-    "bacteroidetes_odb10.2021-02-23.tar.gz",
-    "bacteroidia_odb10.2021-02-23.tar.gz",
-    "baculoviridae_odb10.2020-11-26.tar.gz",
-    "basidiomycota_odb10.2020-09-10.tar.gz",
-    "bclasvirinae_odb10.2020-11-26.tar.gz",
-    "betabaculovirus_odb10.2020-11-26.tar.gz",
-    "betaherpesvirinae_odb10.2020-11-26.tar.gz",
-    "betaproteobacteria_odb10.2021-02-23.tar.gz",
-    "boletales_odb10.2020-08-05.tar.gz",
-    "brassicales_odb10.2020-08-05.tar.gz",
-    "burkholderiales_odb10.2021-02-23.tar.gz",
-    "campylobacterales_odb10.2020-03-06.tar.gz",
-    "capnodiales_odb10.2020-08-05.tar.gz",
-    "carnivora_odb10.2021-02-19.tar.gz",
-    "cellvibrionales_odb10.2020-03-06.tar.gz",
-    "cetartiodactyla_odb10.2021-02-19.tar.gz",
-    "chaetothyriales_odb10.2020-08-05.tar.gz",
-    "cheoctovirus_odb10.2020-11-26.tar.gz",
-    "chlamydiae_odb10.2020-03-06.tar.gz",
-    "chlorobi_odb10.2020-03-06.tar.gz",
-    "chloroflexi_odb10.2020-03-06.tar.gz",
-    "chlorophyta_odb10.2020-08-05.tar.gz",
-    "chordopoxvirinae_odb10.2020-11-26.tar.gz",
-    "chromatiales_odb10.2020-03-06.tar.gz",
-    "chroococcales_odb10.2020-03-06.tar.gz",
-    "clostridia_odb10.2020-03-06.tar.gz",
-    "clostridiales_odb10.2020-03-06.tar.gz",
-    "coccidia_odb10.2020-08-05.tar.gz",
-    "coriobacteriales_odb10.2020-03-06.tar.gz",
-    "coriobacteriia_odb10.2020-03-06.tar.gz",
-    "corynebacteriales_odb10.2020-03-06.tar.gz",
-    "cyanobacteria_odb10.2021-02-23.tar.gz",
-    "cyprinodontiformes_odb10.2021-02-19.tar.gz",
-    "cytophagales_odb10.2021-02-23.tar.gz",
-    "cytophagia_odb10.2021-02-23.tar.gz",
-    "delta-epsilon-subdivisions_odb10.2021-02-23.tar.gz",
-    "deltaproteobacteria_odb10.2021-02-23.tar.gz",
-    "desulfobacterales_odb10.2020-03-06.tar.gz",
-    "desulfovibrionales_odb10.2021-02-23.tar.gz",
-    "desulfurococcales_odb10.2021-02-23.tar.gz",
-    "desulfuromonadales_odb10.2020-03-06.tar.gz",
-    "diptera_odb10.2020-08-05.tar.gz",
-    "dothideomycetes_odb10.2020-08-05.tar.gz",
-    "embryophyta_odb10.2020-09-10.tar.gz",
-    "endopterygota_odb10.2020-09-10.tar.gz",
-    "enquatrovirus_odb10.2021-05-05.tar.gz",
-    "enterobacterales_odb10.2021-02-23.tar.gz",
-    "entomoplasmatales_odb10.2020-03-06.tar.gz",
-    "epsilonproteobacteria_odb10.2020-03-06.tar.gz",
-    "euarchontoglires_odb10.2021-02-19.tar.gz",
-    "eudicots_odb10.2020-09-10.tar.gz",
-    "euglenozoa_odb10.2020-08-05.tar.gz",
-    "eukaryota_odb10.2020-09-10.tar.gz",
-    "eurotiales_odb10.2020-08-05.tar.gz",
-    "eurotiomycetes_odb10.2020-08-05.tar.gz",
-    "euryarchaeota_odb10.2021-02-23.tar.gz",
-    "eutheria_odb10.2021-02-19.tar.gz",
-    "fabales_odb10.2020-08-05.tar.gz",
-    "firmicutes_odb10.2021-02-23.tar.gz",
-    "flavobacteriales_odb10.2021-02-23.tar.gz",
-    "flavobacteriia_odb10.2021-02-23.tar.gz",
-    "fromanvirus_odb10.2020-11-26.tar.gz",
-    "fungi_odb10.2021-06-28.tar.gz",
-    "fusobacteria_odb10.2020-03-06.tar.gz",
-    "fusobacteriales_odb10.2020-03-06.tar.gz",
-    "gammaherpesvirinae_odb10.2020-11-26.tar.gz",
-    "gammaproteobacteria_odb10.2021-02-23.tar.gz",
-    "glires_odb10.2021-02-19.tar.gz",
-    "glomerellales_odb10.2020-08-05.tar.gz",
-    "guernseyvirinae_odb10.2020-11-26.tar.gz",
-    "halobacteria_odb10.2021-02-23.tar.gz",
-    "halobacteriales_odb10.2021-02-23.tar.gz",
-    "haloferacales_odb10.2021-02-23.tar.gz",
-    "helotiales_odb10.2020-08-05.tar.gz",
-    "hemiptera_odb10.2020-08-05.tar.gz",
-    "herpesviridae_odb10.2020-11-26.tar.gz",
-    "hymenoptera_odb10.2020-08-05.tar.gz",
-    "hypocreales_odb10.2020-08-05.tar.gz",
-    "insecta_odb10.2020-09-10.tar.gz",
-    "iridoviridae_odb10.2020-11-26.tar.gz",
-    "lactobacillales_odb10.2020-03-06.tar.gz",
-    "laurasiatheria_odb10.2021-02-19.tar.gz",
-    "legionellales_odb10.2020-03-06.tar.gz",
-    "leotiomycetes_odb10.2020-08-05.tar.gz",
-    "lepidoptera_odb10.2020-08-05.tar.gz",
-    "liliopsida_odb10.2020-09-10.tar.gz",
-    "mammalia_odb10.2021-02-19.tar.gz",
-    "metazoa_odb10.2021-02-24.tar.gz",
-    "methanobacteria_odb10.2021-02-23.tar.gz",
-    "methanococcales_odb10.2021-02-23.tar.gz",
-    "methanomicrobia_odb10.2021-02-23.tar.gz",
-    "methanomicrobiales_odb10.2021-02-23.tar.gz",
-    "micrococcales_odb10.2021-02-23.tar.gz",
-    "microsporidia_odb10.2020-08-05.tar.gz",
-    "mollicutes_odb10.2020-03-06.tar.gz",
-    "mollusca_odb10.2020-08-05.tar.gz",
-    "mucorales_odb10.2020-08-05.tar.gz",
-    "mucoromycota_odb10.2020-08-05.tar.gz",
-    "mycoplasmatales_odb10.2020-03-06.tar.gz",
-    "natrialbales_odb10.2021-02-23.tar.gz",
-    "neisseriales_odb10.2021-02-23.tar.gz",
-    "nematoda_odb10.2020-08-05.tar.gz",
-    "nitrosomonadales_odb10.2020-03-06.tar.gz",
-    "nostocales_odb10.2020-03-06.tar.gz",
-    "oceanospirillales_odb10.2020-03-06.tar.gz",
-    "onygenales_odb10.2020-08-05.tar.gz",
-    "oscillatoriales_odb10.2021-02-23.tar.gz",
-    "pahexavirus_odb10.2020-11-26.tar.gz",
-    "passeriformes_odb10.2021-02-19.tar.gz",
-    "pasteurellales_odb10.2021-02-23.tar.gz",
-    "peduovirus_odb10.2021-02-23.tar.gz",
-    "planctomycetes_odb10.2020-03-06.tar.gz",
-    "plasmodium_odb10.2020-08-05.tar.gz",
-    "pleosporales_odb10.2020-08-05.tar.gz",
-    "poales_odb10.2020-08-05.tar.gz",
-    "polyporales_odb10.2020-08-05.tar.gz",
-    "poxviridae_odb10.2020-11-26.tar.gz",
-    "primates_odb10.2021-02-19.tar.gz",
-    "propionibacteriales_odb10.2020-03-06.tar.gz",
-    "proteobacteria_odb10.2021-02-23.tar.gz",
-    "pseudomonadales_odb10.2020-03-06.tar.gz",
-    "rhizobiales_odb10.2020-03-06.tar.gz",
-    "rhizobium-agrobacterium_group_odb10.2020-03-06.tar.gz",
-    "rhodobacterales_odb10.2021-02-23.tar.gz",
-    "rhodospirillales_odb10.2020-03-06.tar.gz",
-    "rickettsiales_odb10.2020-03-06.tar.gz",
-    "rudiviridae_odb10.2020-11-26.tar.gz",
-    "saccharomycetes_odb10.2020-08-05.tar.gz",
-    "sauropsida_odb10.2021-02-19.tar.gz",
-    "selenomonadales_odb10.2020-03-06.tar.gz",
-    "simplexvirus_odb10.2020-11-26.tar.gz",
-    "skunavirus_odb10.2020-11-26.tar.gz",
-    "solanales_odb10.2020-08-05.tar.gz",
-    "sordariomycetes_odb10.2020-08-05.tar.gz",
-    "sphingobacteriia_odb10.2020-03-06.tar.gz",
-    "sphingomonadales_odb10.2021-02-23.tar.gz",
-    "spirochaetales_odb10.2020-03-06.tar.gz",
-    "spirochaetes_odb10.2021-02-23.tar.gz",
-    "spirochaetia_odb10.2021-02-23.tar.gz",
-    "spounavirinae_odb10.2020-11-26.tar.gz",
-    "stramenopiles_odb10.2020-08-05.tar.gz",
-    "streptomycetales_odb10.2020-03-06.tar.gz",
-    "streptosporangiales_odb10.2020-03-06.tar.gz",
-    "sulfolobales_odb10.2021-02-23.tar.gz",
-    "synechococcales_odb10.2020-03-06.tar.gz",
-    "synergistetes_odb10.2020-03-06.tar.gz",
-    "tenericutes_odb10.2020-03-06.tar.gz",
-    "tequatrovirus_odb10.2020-11-26.tar.gz",
-    "teseptimavirus_odb10.2020-11-26.tar.gz",
-    "tetrapoda_odb10.2021-02-19.tar.gz",
-    "tevenvirinae_odb10.2021-02-23.tar.gz",
-    "thaumarchaeota_odb10.2021-02-23.tar.gz",
-    "thermoanaerobacterales_odb10.2020-03-06.tar.gz",
-    "thermoplasmata_odb10.2021-02-23.tar.gz",
-    "thermoproteales_odb10.2021-02-23.tar.gz",
-    "thermoprotei_odb10.2021-02-23.tar.gz",
-    "thermotogae_odb10.2020-03-06.tar.gz",
-    "thiotrichales_odb10.2020-03-06.tar.gz",
-    "tissierellales_odb10.2020-03-06.tar.gz",
-    "tissierellia_odb10.2020-03-06.tar.gz",
-    "tremellomycetes_odb10.2020-08-05.tar.gz",
-    "tunavirinae_odb10.2020-11-26.tar.gz",
-    "varicellovirus_odb10.2020-11-26.tar.gz",
-    "verrucomicrobia_odb10.2020-03-06.tar.gz",
-    "vertebrata_odb10.2021-02-19.tar.gz",
-    "vibrionales_odb10.2020-03-06.tar.gz",
-    "viridiplantae_odb10.2020-09-10.tar.gz",
-    "xanthomonadales_odb10.2020-03-06.tar.gz",
-]
-
-
-def download_file(url, dest):
-    with requests.get(url, stream=True) as r:
-        r.raise_for_status()
-        with open(dest, 'wb') as f:
-            for chunk in r.iter_content(chunk_size=8192):
-                f.write(chunk)
-
-
-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('--wget', dest='wget', action='store_true', help='Download using wget (instead of urllib)')
-    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']
-    if args.wget:
-        cmd_args += ['--wget']
-    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)
-
-    # Download newer busco datasets from orthodb 10
-    if args.partial:
-        BUSCO_10_DATASETS = BUSCO_10_DATASETS[:1]
-
-    for busco_dataset in BUSCO_10_DATASETS:
-        print("Downloading additional busco orthodb10 dataset %s" % busco_dataset)
-        dest_tar = os.path.join(output_directory, busco_dataset)
-        download_file(BUSCO_10_DATASETS_URL.format(dataset=busco_dataset), dest_tar)
-        print("Extracting %s" % busco_dataset)
-        tar = tarfile.open(dest_tar, "r:gz")
-        tar.extractall(output_directory)
-        tar.close()
-        os.remove(dest_tar)
-
-    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)
--- a/data_manager/funannotate.xml	Fri Nov 19 15:43:06 2021 +0000
+++ b/data_manager/funannotate.xml	Fri Mar 07 22:33:21 2025 +0000
@@ -1,23 +1,47 @@
-<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01">
+<tool id="data_manager_funannotate" name="Funannotate data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
+    <macros>
+        <token name="@TOOL_VERSION@">1.8.15</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.8.9">funannotate</requirement>
-        <requirement type="package" version="2.26.0">requests</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
     </requirements>
     <version_command>funannotate check --show-versions</version_command>
     <command detect_errors="exit_code"><![CDATA[
-#if $wget:
-    ## Asked for wget, we assume there's a certificate problem on (at least) one
-    ## of the many requested servers, force disable of all checks
-    echo "check_certificate = off" > \$HOME/.wgetrc &&
-#end if
+        #if $wget:
+            ## Asked for wget, we assume there's a certificate problem on (at least) one
+            ## of the many requested servers, force disable of all checks
+            echo "check_certificate = off" > \$HOME/.wgetrc &&
+        #end if
 
-python -u '$__tool_directory__/funannotate.py'
-$partial_data
-$wget
-\$(date +'%Y-%m-%d-%H%M%S')
-'funannotate'
-'${output_file}'
+        funannotate setup
+            -d '$output_file.extra_files_path'
+        #if $partial_data
+            -i merops -b eukaryota
+        #else
+            -b all
+        #end if
+            $wget
+        &&
+        cp '$dmjson' '$output_file'
     ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import datetime
+#set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
+    {
+      "data_tables":{
+        "funannotate":[
+          {
+            "value":"$version_id",
+            "description":"Funannotate database $version_id",
+            "format_version":"1.0",
+            "path":"$output_file.extra_files_path"
+          }
+        ]
+      }
+    }]]></configfile>
+    </configfiles>
     <inputs>
         <param name="partial_data" type="hidden" value="" help="Used for testing"/>
         <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
@@ -31,7 +55,7 @@
             <output name="output_file">
                 <assert_contents>
                     <has_text text="Funannotate database "/>
-                    <has_text text='"format_version": "1.0"'/>
+                    <has_text text='"format_version":"1.0"'/>
                 </assert_contents>
             </output>
         </test>
@@ -41,7 +65,7 @@
             <output name="output_file">
                 <assert_contents>
                     <has_text text="Funannotate database "/>
-                    <has_text text='"format_version": "1.0"'/>
+                    <has_text text='"format_version":"1.0"'/>
                 </assert_contents>
             </output>
         </test>
--- a/test-data/funannotate.loc	Fri Nov 19 15:43:06 2021 +0000
+++ b/test-data/funannotate.loc	Fri Mar 07 22:33:21 2025 +0000
@@ -7,3 +7,10 @@
 # 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
+2025-02-17-000000	Funannotate database 2025-02-17-000000		/tmp/tmpm1ezjinx/galaxy-dev/tool-data/funannotate/2025-02-17-000000
+2025-02-17-210445	Funannotate database 2025-02-17-210445		/tmp/tmpg0tuguj6/galaxy-dev/tool-data/funannotate/2025-02-17-210445
+2025-02-17-210504	Funannotate database 2025-02-17-210504		/tmp/tmpg0tuguj6/galaxy-dev/tool-data/funannotate/2025-02-17-210504
+2025-02-17-210714	Funannotate database 2025-02-17-210714	1.0	/tmp/tmpdtjxf3c7/galaxy-dev/tool-data/funannotate/2025-02-17-210714
+2025-02-17-210732	Funannotate database 2025-02-17-210732	1.0	/tmp/tmpdtjxf3c7/galaxy-dev/tool-data/funannotate/2025-02-17-210732
+2025-02-17-211010	Funannotate database 2025-02-17-211010	1.0	/tmp/tmp07fm9fgh/galaxy-dev/tool-data/funannotate/2025-02-17-211010
+2025-02-17-211028	Funannotate database 2025-02-17-211028	1.0	/tmp/tmp07fm9fgh/galaxy-dev/tool-data/funannotate/2025-02-17-211028