Mercurial > repos > iuc > data_manager_mmseqs2_database

changeset 2:35885ec2e59b 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/master/data_managers/data_manager_mmseqs2_database commit 611b90f1628037f05d85905c88629a422d0a2053
author iuc
date Mon, 14 Apr 2025 18:39:14 +0000
parents 561c4b181bfa
children
files data_manager/data_manager_mmseqs2_download.xml test-data/mmseqs2_databases.loc.test
diffstat 2 files changed, 9 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_mmseqs2_download.xml	Thu Mar 27 16:42:41 2025 +0000
+++ b/data_manager/data_manager_mmseqs2_download.xml	Mon Apr 14 18:39:14 2025 +0000
@@ -1,7 +1,7 @@
 <tool id="data_manager_mmseqs2_download" name="Download MMseqs2 databases" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
     <description></description>
     <macros>
-        <token name="@TOOL_VERSION@">15.6f452</token>
+        <token name="@TOOL_VERSION@">17-b804f</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -40,9 +40,9 @@
     <inputs>
         <conditional name="db_name">
             <param argument="type" type="select" label="Type of Databases">
-                <option value="aminoacid">Aminoacid databases</option>
+                <option value="aminoacid">Aminoacid databases without taxonomy</option>
                 <option value="aminoacid_taxonomy">Aminoacid databases that can be used for taxonomy</option>
-                <option value="nucleotide">Nucleotide databases</option>
+                <option value="nucleotide">Nucleotide databases without taxonomy</option>
                 <option value="nucleotide_taxonomy">Nucleotide databases that can be used for taxonomy</option>
                 <option value="profile">Profile databases</option>
             </param>
@@ -50,14 +50,6 @@
                 <param name="db_type" value="aminoacid" type="hidden"/>
                 <param name="db_taxonomy" value="no" type="hidden"/>
                 <param name="database" type="select" label="MMseqs2 aminoacid databases">
-                    <option value="UniRef100" selected="true">UniRef100</option>
-                    <option value="UniRef90">UniRef90</option>
-                    <option value="UniRef50">UniRef50</option>
-                    <option value="UniProtKB">UniProtKB</option>
-                    <option value="UniProtKB/TrEMBL">TrEMBL (UniProtKB)</option>
-                    <option value="UniProtKB/Swiss-Prot">Swiss-Prot (UniProtKB)</option>
-                    <option value="NR">NR (Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq)</option>
-                    <option value="GTDB">GTDB (Genome Taxonomy Database)</option>
                     <option value="PDB">PDB (The Protein Data Bank)</option>            
                 </param>
             </when>
@@ -79,8 +71,6 @@
                 <param name="db_type" value="nucleotide" type="hidden"/>
                 <param name="db_taxonomy" value="no" type="hidden"/>
                 <param name="database" type="select" label="MMseqs2 nucleotide databases">
-                    <option value="SILVA">SILVA</option>
-                    <option value="Kalamari">Kalamari</option>
                     <option value="NT">NT (Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ excluding GSS, STS, PAT, EST, HTG, and WGS)</option>
                     <option value="Resfinder">Resfinder</option>
                 </param>
@@ -122,8 +112,8 @@
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"mmseqs2_databases":'/>
-                    <has_text text='"version": "15.6f452"'/>
-                    <has_text_matching expression='"value": "SILVA-15.6f452-[0-9]{8}"'/>
+                    <has_text text='"version": "@TOOL_VERSION@"'/>
+                    <has_text_matching expression='"value": "SILVA-@TOOL_VERSION@-[0-9]{8}"'/>
                     <has_text_matching expression='"name": "SILVA [0-9]{8}"'/>
                     <has_text text='"type": "nucleotide"'/>
                     <has_text text='"taxonomy": "yes"'/>
@@ -141,8 +131,8 @@
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"mmseqs2_databases":'/>
-                    <has_text text='"version": "15.6f452"'/>
-                    <has_text_matching expression='"value": "UniProtKB/Swiss-Prot-15.6f452-[0-9]{8}"'/>
+                    <has_text text='"version": "@TOOL_VERSION@"'/>
+                    <has_text_matching expression='"value": "UniProtKB/Swiss-Prot-@TOOL_VERSION@-[0-9]{8}"'/>
                     <has_text_matching expression='"name": "UniProtKB/Swiss-Prot [0-9]{8}"'/>
                     <has_text text='"type": "aminoacid"'/>
                     <has_text text='"taxonomy": "yes"'/>
--- a/test-data/mmseqs2_databases.loc.test	Thu Mar 27 16:42:41 2025 +0000
+++ b/test-data/mmseqs2_databases.loc.test	Mon Apr 14 18:39:14 2025 +0000
@@ -1,2 +1,2 @@
-SILVA-15.6f452-10022025	SILVA 10022025	nucleotide	yes	/tmp/tmpepbr4_rb/galaxy-dev/tool-data/mmseqs2/SILVA	15.6f452
-UniProtKB/Swiss-Prot-15.6f452-10022025	UniProtKB/Swiss-Prot 10022025	aminoacid	yes	/tmp/tmpepbr4_rb/galaxy-dev/tool-data/mmseqs2/Swiss-Prot	15.6f452
+SILVA-17-b804f-31032025	SILVA 31032025	nucleotide	yes	/tmp/tmpq6ksdjel/galaxy-dev/tool-data/mmseqs2/SILVA	17-b804f
+UniProtKB/Swiss-Prot-17-b804f-31032025	UniProtKB/Swiss-Prot 31032025	aminoacid	yes	/tmp/tmpq6ksdjel/galaxy-dev/tool-data/mmseqs2/Swiss-Prot	17-b804f