delete useless files and parameters + last tests

galaxyproject · Nov 19, 2024 · 220cd5a · 220cd5a
1 parent 78ba0c6
commit 220cd5a
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Showing 9 changed files with 2 additions and 8,973 deletions.
diff --git a/data_managers/data_manager_mmseqs2_database/data_manager/data_manager_mmseqs2_download.xml b/data_managers/data_manager_mmseqs2_database/data_manager/data_manager_mmseqs2_download.xml
@@ -5,20 +5,6 @@
         <token name="@VERSION_SUFFIX@">0</token>
         <token name="@COMMIT@">6f452</token>
         <token name="@FULL_TOOL_VERSION@">@TOOL_VERSION@.@COMMIT@</token>
-        <token name="@AMINOACID_TAXO_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>
-        </token>
-        <token name="@NUCLEOTIDE_TAXO_DATABASES@">
-            <option value="SILVA">SILVA</option>
-            <option value="Kalamari">Kalamari</option>
-        </token>
     </macros>
     <requirements>
         <requirement type="package" version="@FULL_TOOL_VERSION@">mmseqs2</requirement>

diff --git a/...ers/data_manager_mmseqs2_database/test-data/mmseqs2_aminoacid_taxonomy_databases.loc.test b/...ers/data_manager_mmseqs2_database/test-data/mmseqs2_aminoacid_taxonomy_databases.loc.test
@@ -1,2 +1,3 @@
 UniProtKB/Swiss-Prot-15.6f452-15112024	UniProtKB/Swiss-Prot 15112024		/tmp/tmp5_ppo41w/galaxy-dev/tool-data/Swiss-Prot	15.6f452
 UniProtKB/Swiss-Prot-15.6f452-18112024	UniProtKB/Swiss-Prot 18112024		/tmp/tmpm3q21te0/galaxy-dev/tool-data/Swiss-Prot	15.6f452
+UniProtKB/Swiss-Prot-15.6f452-19112024	UniProtKB/Swiss-Prot 19112024		/tmp/tmprct41jv5/galaxy-dev/tool-data/Swiss-Prot	15.6f452
diff --git a/...rs/data_manager_mmseqs2_database/test-data/mmseqs2_nucleotide_taxonomy_databases.loc.test b/...rs/data_manager_mmseqs2_database/test-data/mmseqs2_nucleotide_taxonomy_databases.loc.test
@@ -1 +1,2 @@
 SILVA-15.6f452-18112024	SILVA 18112024		/tmp/tmpm3q21te0/galaxy-dev/tool-data/SILVA	15.6f452
+SILVA-15.6f452-19112024	SILVA 19112024		/tmp/tmprct41jv5/galaxy-dev/tool-data/SILVA	15.6f452
diff --git a/tools/mmseqs2/mmseqs2_easy_taxonomy_assignment.xml b/tools/mmseqs2/mmseqs2_easy_taxonomy_assignment.xml
diff --git a/tools/mmseqs2/test-data/result_krona_report b/tools/mmseqs2/test-data/result_krona_report
diff --git a/tools/mmseqs2/test-data/result_lca.tsv b/tools/mmseqs2/test-data/result_lca.tsv
diff --git a/tools/mmseqs2/test-data/result_report b/tools/mmseqs2/test-data/result_report
diff --git a/tools/mmseqs2/test-data/result_tophit_aln b/tools/mmseqs2/test-data/result_tophit_aln
diff --git a/tools/mmseqs2/test-data/result_tophit_report b/tools/mmseqs2/test-data/result_tophit_report