try symlink with a directory

galaxyproject · Nov 21, 2024 · 54a432f · 54a432f
1 parent 072fc28
commit 54a432f
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Showing 11 changed files with 14 additions and 10 deletions.
diff --git a/tools/mmseqs2/mmseqs2_taxonomy_assignment.xml b/tools/mmseqs2/mmseqs2_taxonomy_assignment.xml
@@ -14,12 +14,14 @@ mmseqs createdb
     'input'
     'sequenceDB'
     --dbtype '$createdb.dbtype'
+    --createdb-mode $createdb.createdb_mode
     --shuffle $createdb.shuffle &&
-ls -lah &&
-ls -lah '$createtaxdb.database_type.mmseqs2_db_select.fields.path'* &&
+ls -lah '$createtaxdb.database_type.mmseqs2_db_select.fields.path' &&
 ln -s  '$createtaxdb.database_type.mmseqs2_db_select.fields.path' taxdb &&
+ls -lah &&
+ls -lah taxdb &&
 mmseqs createtaxdb
-    'taxdb'
+    'taxdb'/database
     'tmp'
     #if '$createtaxdb.tax_mapping_file'
     --tax-mapping-file '$createtaxdb.tax_mapping_file'
@@ -34,16 +36,14 @@ mmseqs createtaxdb
                 --taxon-list '$filtertaxseqdb.filtertaxseqdb_bool.use_filter.taxon_list' &&
             #end if
     #end if
-chmod -Rv 766 '$createtaxdb.database_type.mmseqs2_db_select.fields.path'_taxonomy &&
-ls -lah &&
-ls -lah '$createtaxdb.database_type.mmseqs2_db_select.fields.path'* &&
+ls -lah taxdb &&
 mmseqs taxonomy
     #if str($filtertaxseqdb.filtertaxseqdb_bool.use_filter) == "yes"
         'sequenceDB_filtered'
     #else 
         'sequenceDB'
     #end if
-    '$createtaxdb.database_type.mmseqs2_db_select.fields.path'
+    'taxdb'/database
     'output_taxonomy'
     'tmp'
     #if str($taxonomy.alph_type.type) == "amino_acid"
@@ -195,7 +195,7 @@ mmseqs createtsv
 #if str($kraken_report.keep_report) == "Yes"
 &&
     mmseqs taxonomyreport
-        '$createtaxdb.database_type.mmseqs2_db_select.fields.path'
+        'taxdb'/database
         'output_taxonomy'
         'taxo_result.txt'
         --report-mode 0
@@ -204,7 +204,7 @@ mmseqs createtsv
 #if str($krona_report.keep_report) == "Yes"
 &&
     mmseqs taxonomyreport
-        '$createtaxdb.database_type.mmseqs2_db_select.fields.path'
+        'taxdb'/database
         'output_taxonomy'
         'taxo_result.html'
         --report-mode 1
@@ -215,12 +215,16 @@ mmseqs createtsv
     ]]></command>
     <inputs>
         <section name="createdb" title="Convert FASTA/Q file(s) to MMseqs sequence DB format"  expanded="true">
-            <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Input fasta file" help="" />
+            <param name="input_fasta" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input fasta file" help="" />
             <param argument="--dbtype" type="select" label="Input type" help="" >
                 <option value="0" selected="true">Auto</option>
                 <option value="1">Amino acid</option>
                 <option value="2">Nucleotides</option>
             </param>
+            <param argument="--createdb-mode" type="select" label="Create DB mode" help="" >
+                <option value="0" selected="true">Copy data</option>
+                <option value="1">Soft link data and write new index (works only with single line fasta/q)</option>
+            </param>
             <param argument="--shuffle" type="boolean" checked="true" label="Shuffle input database" truevalue="1" falsevalue="0" optional="true" help="" />
         </section>
         <section name="createtaxdb" title="Add taxonomic labels to reference sequence DB" expanded="true">

diff --git a/tools/mmseqs2/test-data/Swiss-Prot → tools/mmseqs2/test-data/Swiss-Prot/database b/tools/mmseqs2/test-data/Swiss-Prot → tools/mmseqs2/test-data/Swiss-Prot/database
diff --git a/tools/mmseqs2/test-data/Swiss-Prot.dbtype → ...eqs2/test-data/Swiss-Prot/database.dbtype b/tools/mmseqs2/test-data/Swiss-Prot.dbtype → ...eqs2/test-data/Swiss-Prot/database.dbtype
diff --git a/tools/mmseqs2/test-data/Swiss-Prot.index → ...seqs2/test-data/Swiss-Prot/database.index b/tools/mmseqs2/test-data/Swiss-Prot.index → ...seqs2/test-data/Swiss-Prot/database.index
diff --git a/tools/mmseqs2/test-data/Swiss-Prot.lookup → ...eqs2/test-data/Swiss-Prot/database.lookup b/tools/mmseqs2/test-data/Swiss-Prot.lookup → ...eqs2/test-data/Swiss-Prot/database.lookup
diff --git a/tools/mmseqs2/test-data/Swiss-Prot.source → ...eqs2/test-data/Swiss-Prot/database.source b/tools/mmseqs2/test-data/Swiss-Prot.source → ...eqs2/test-data/Swiss-Prot/database.source
diff --git a/tools/mmseqs2/test-data/Swiss-Prot.version → ...qs2/test-data/Swiss-Prot/database.version b/tools/mmseqs2/test-data/Swiss-Prot.version → ...qs2/test-data/Swiss-Prot/database.version
diff --git a/tools/mmseqs2/test-data/Swiss-Prot_h → ...s/mmseqs2/test-data/Swiss-Prot/database_h b/tools/mmseqs2/test-data/Swiss-Prot_h → ...s/mmseqs2/test-data/Swiss-Prot/database_h
diff --git a/tools/mmseqs2/test-data/Swiss-Prot_h.dbtype → ...s2/test-data/Swiss-Prot/database_h.dbtype b/tools/mmseqs2/test-data/Swiss-Prot_h.dbtype → ...s2/test-data/Swiss-Prot/database_h.dbtype
diff --git a/tools/mmseqs2/test-data/Swiss-Prot_h.index → ...qs2/test-data/Swiss-Prot/database_h.index b/tools/mmseqs2/test-data/Swiss-Prot_h.index → ...qs2/test-data/Swiss-Prot/database_h.index
diff --git a/tools/mmseqs2/test-data/Swiss-Prot_mapping → ...qs2/test-data/Swiss-Prot/database_mapping b/tools/mmseqs2/test-data/Swiss-Prot_mapping → ...qs2/test-data/Swiss-Prot/database_mapping