Mercurial > repos > iuc > data_manager_dada2

changeset 9:f15270614b1b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
author iuc
date Fri, 12 Dec 2025 09:07:08 +0000
parents 0181efacb40a
children
files data_manager/dada2_fetcher.xml
diffstat 1 files changed, 34 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/dada2_fetcher.xml	Sat Nov 22 20:07:44 2025 +0000
+++ b/data_manager/dada2_fetcher.xml	Fri Dec 12 09:07:08 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.2" profile="24.2">
+<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.3" profile="24.2">
     <description>Download reference databases</description>
     <requirements>
         <requirement type="package" version="1.25.0">wget</requirement>
@@ -23,6 +23,8 @@
     "rdp_19_toSpecies": "https://zenodo.org/records/14168771/files/rdp_19_toSpecies_trainset.fa.gz?download=1",
     "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
     "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
+    "unite_10.0_eukaryotes-2025-02-19": "https://s3.hpc.ut.ee/plutof-public/original/e861a3d6-54f4-42dc-882a-5f129beac39a.tgz",
+    "unite_10.0_eukaryotes_singletons-2025-02-19": "https://s3.hpc.ut.ee/plutof-public/original/b02db549-5f04-43fc-afb6-02888b594d10.tgz",
     "unite_8.0_fungi": "https://s3.hpc.ut.ee/plutof-public/original/9f7b41c3-825b-4db8-9c52-74a4603a860a.zip",
     "unite_8.0_fungi_singletons": "https://s3.hpc.ut.ee/plutof-public/original/53dfc9ce-9cb5-4205-84bb-f47faff26462.zip",
     "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
@@ -55,7 +57,7 @@
 cd '${out_file.extra_files_path}' &&
 #for $database in $taxonomy_databases:
     wget '$FILE2TAXURL[str($database)]' -O '${database}.taxonomy' &&
-    #if str($database).startswith("unite")
+    #if str($database).startswith("unite_8.0")
         unzip -p '${database}.taxonomy' "*.fasta" -x "developer/*" > tmp &&
         mv tmp '${database}.taxonomy' &&
     #end if
@@ -93,6 +95,8 @@
     "greengenes_13.84": "GreenGenes version 13.84",
     "greengenes2_2024.09_toGenus": "GreenGenes2 release 2024.09 to Genus (for short reads)",
     "greengenes2_2024.09_toSpecies": "GreenGenes2 release 2024.09 to Species (for long reads)",
+    "unite_10.0_eukaryotes-2025-02-19": "UNITE: General Fasta release 10.0 (2025-02-19) for Eukaroyes",
+    "unite_10.0_eukaryotes_singletons-2025-02-19": "UNITE: General Fasta release 10.0 (2025-02-19) for Eukaroyes including global and 97% singletons",
     "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi",
     "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons",
     "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)",
@@ -164,8 +168,10 @@
             <option value="greengenes2_2024.09_toGenus">GreenGenes2 2024.09 to Genus (for short reads)</option>
             <option value="greengenes2_2024.09_toSpecies">GreenGenes2 2024.09 to Species (for long reads)</option>
             <option value="greengenes_13.84">GreenGenes 13.84</option>
-            <option value="unite_8.0_fungi">UNITE Fungi: General Fasta 8.0 for Fungi</option>
-            <option value="unite_8.0_fungi_singletons">UNITE Fungi: General Fasta release 8.0 for Fungi including global and 97% singletons</option>
+            <option value="unite_10.0_eukaryotes-2025-02-19">UNITE General Fasta 10.0 (2025-02-19) for Eukaryota</option>
+            <option value="unite_10.0_eukaryotes_singletons-2025-02-19">UNITE: General Fasta release 10.0 (2025-02-19) for Eukaryota including global and 97% singletons</option>
+            <option value="unite_8.0_fungi">UNITE: General Fasta 8.0 for Fungi</option>
+            <option value="unite_8.0_fungi_singletons">UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons</option>
             <!-- UNITE Eukaryotes not yet supported https://github.com/benjjneb/dada2/issues/702 -->
             <option value="RefSeq_RDP_2018_05">NCBI RefSeq 16S rRNA database supplemented by RDP 05/2018</option>
             <option value="gtdb_202_toGenus">GTDB: Genome Taxonomy Database 202 to Genus (for short reads) </option>
@@ -292,6 +298,30 @@
             </assert_command>
         </test>
         <test>
+            <param name="taxonomy_databases" value="unite_10.0_eukaryotes-2025-02-19"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"value": "unite_10.0_eukaryotes-2025-02-19"'/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="wget" n="1"/>
+                <has_text text="unzip" negate="true"/>
+            </assert_command>
+        </test>
+        <test>
+            <param name="taxonomy_databases" value="unite_10.0_eukaryotes_singletons-2025-02-19"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"value": "unite_10.0_eukaryotes_singletons-2025-02-19"'/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="wget" n="1"/>
+            </assert_command>
+        </test>
+
+        <test>
             <param name="taxonomy_databases" value="unite_8.0_fungi"/>
             <output name="out_file" file="unite8fungi_json"/>
             <assert_command>