diamond: added tax test and test data correction

- prot.accession2taxid was missing the header: bbuchfink/diamond#217 - added test for taxonomic selection by list of ids
bgruening · Aug 31, 2018 · 6f0b384 · 6f0b384
1 parent 982bb1c
commit 6f0b384
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Showing 4 changed files with 37 additions and 1 deletion.
diff --git a/tools/diamond/diamond.xml b/tools/diamond/diamond.xml
@@ -233,6 +233,40 @@
             <param name="block_size" value="2"/>
             <output name="blast_tabular" file="diamond_results.tabular"/>
         </test>
+        <test>
+            <conditional name="method_cond">
+                <param name="method_select" value="blastp" />
+            </conditional>
+            <param name="query" value="protein.fasta" ftype="fasta"/>
+            <conditional name="ref_db_source">
+                <param name="db_source" value="history"/>
+                <param name="reference_database" value="db-wtax.dmnd"/>
+            </conditional>
+            <conditional name="tax_cond">
+		    <param name="tax_select" value="list"/>
+                    <param name="taxonlist" value="2" />
+            </conditional>
+            <conditional name="output">
+                <param name="outfmt" value="6"/>
+                <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
+            </conditional>
+            <param name="sensitivity" value="0"/>
+            <param name="matrix" value="BLOSUM62"/>
+            <param name="comp-based-stat" value="1"/>
+            <param name="masking" value="1"/>
+            <conditional name="hit_filter">
+                <param name="hit_filter_select" value="max"/>
+                <param name="max_target_seqs" value="25" />
+            </conditional>
+            <conditional name="filter_score">
+                <param name="filter_score_select" value="evalue"/>
+                <param name="evalue" value="0.001" />
+            </conditional>
+            <param name="id" value="0"/>
+            <param name="query_cover" value="0"/>
+            <param name="block_size" value="2"/>
+            <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
+        </test>
         <test>
             <conditional name="method_cond">
                 <param name="method_select" value="blastx" />
@@ -272,7 +306,7 @@
             <param name="query" value="protein.fasta" ftype="fasta"/>
             <conditional name="ref_db_source">
                 <param name="db_source" value="history"/>
-                <param name="reference_database" value="db.dmnd"/>
+                <param name="reference_database" value="db-wtax.dmnd"/>
             </conditional>
             <conditional name="output">
                 <param name="outfmt" value="100"/>

diff --git a/tools/diamond/test-data/db-wtax.dmnd b/tools/diamond/test-data/db-wtax.dmnd
diff --git a/tools/diamond/test-data/diamond_results.wtax.tabular b/tools/diamond/test-data/diamond_results.wtax.tabular
@@ -0,0 +1 @@
+sequence	gi|5524211|gb|AAD44166.1|	99.6	284	0	1	1	283	1	284	2.0e-158	541.2
diff --git a/tools/diamond/test-data/prot.accession2taxid b/tools/diamond/test-data/prot.accession2taxid
@@ -1,3 +1,4 @@
+accession	accession.version	taxid	gi
 AAD44166	AAD44166.1	2	5524211
 AAD44167	AAD44167.1	3	5524212