Mercurial > repos > iuc > lexicmap

changeset 2:d1a30eb26392 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
author iuc
date Thu, 18 Sep 2025 11:27:52 +0000
parents c5b3d5e02f5a
children cefde4c7f92e
files lexicmap.xml macros.xml test-data/lexicmap_query2.fasta.gz test-data/lexicmap_query_result2.tsv
diffstat 4 files changed, 23 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/lexicmap.xml	Tue Sep 16 14:27:49 2025 +0000
+++ b/lexicmap.xml	Thu Sep 18 11:27:52 2025 +0000
@@ -21,7 +21,11 @@
         --index '${db_opts.lexicmap_index.fields.path}'
     #end if
 
-    '$query' --out-file '$out_file'
+    #for $q in $query
+        '$q'
+    #end for
+
+    --out-file '$out_file'
 
     --top-n-genomes '$top_n_genomes'
 
@@ -96,6 +100,7 @@
         </data>
     </outputs>
     <tests>
+        <!-- Test 1 - query a local index with one query -->
         <test expect_num_outputs="1">
             <conditional name="db_opts">
                 <param name="db_opts_selector" value="db"/>
@@ -107,6 +112,19 @@
             </section>
             <output name="out_file" value="lexicmap_query_result.tsv" />
         </test>
+        <!-- Test 2 - query a local index with multiple query files -->
+        <test expect_num_outputs="1">
+            <conditional name="db_opts">
+                <param name="db_opts_selector" value="db"/>
+                <param name="lexicmap_index" value="LexicMapIndex1" />
+            </conditional>
+            <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz" />
+            <section name="advanced_settings">
+                <param name="load_whole_seeds" value="true" />
+            </section>
+            <output name="out_file" value="lexicmap_query_result2.tsv" />
+        </test>
+        <!-- Test 3 - query a  index found in the history with one query -->
         <test expect_num_outputs="1">
             <conditional name="db_opts">
                 <param name="db_opts_selector" value="histdb"/>
--- a/macros.xml	Tue Sep 16 14:27:49 2025 +0000
+++ b/macros.xml	Thu Sep 18 11:27:52 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.7.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE_VERSION@">25.0</token>
     <token name="@FASTA_TYPES@">fasta.gz,fasta</token>
     <xml name="requirements">
Binary file test-data/lexicmap_query2.fasta.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lexicmap_query_result2.tsv	Thu Sep 18 11:27:52 2025 +0000
@@ -0,0 +1,3 @@
+query	qlen	hits	sgenome	sseqid	qcovGnm	cls	hsp	qcovHSP	alenHSP	pident	gaps	qstart	qend	sstart	send	sstr	slen	evalue	bitscore
+query1	240	1	dataset_963f49fd-cb75-4b60-909c-e63a9651ba65	NC_028981.1	100.000	1	1	100.000	240	100.000	0	1	240	2001	2240	+	7417	3.76e-125	434
+query2	320	1	dataset_963f49fd-cb75-4b60-909c-e63a9651ba65	NC_028981.1	100.000	1	1	100.000	320	100.000	0	1	320	6161	6480	+	7417	1.86e-168	578