barcode test

usegalaxy-au · Jun 17, 2024 · 332e72b · 332e72b
1 parent a80d7a9
commit 332e72b
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Showing 5 changed files with 33 additions and 1 deletion.
diff --git a/tools/dorado/dorado_pod5_convert.xml b/tools/dorado/dorado_pod5_convert.xml
@@ -27,7 +27,7 @@ input.fast5
     <tests>
         <test expect_num_outputs="1">
             <param name="fast5_in" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5"/>
-            <output name="pod5_out" file="dorado_pod5_convert.test1.out.pod5"/>
+            <output name="pod5_out" file="dorado_pod5_convert.test1.out.pod5" ftype="fast5"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/dorado/test-data/dorado.test1.out.tsv b/tools/dorado/test-data/dorado.test1.out.tsv
@@ -0,0 +1,11 @@
+filename	read_id	run_id	channel	mux	start_time	duration	template_start	template_duration	sequence_length_template	mean_qscore_template	barcode
+reads.pod5	0067486b-9f92-4849-8456-671463e64412	473bf0edfc2f8f756173de35db5da9b6f6db4959	84	4	164.018	2.33125	164.249	2.1	884	12.2444	unclassified
+reads.pod5	0072b26f-f37c-4517-afa7-621543ac2187	473bf0edfc2f8f756173de35db5da9b6f6db4959	317	3	111.275	2.31875	111.492	2.10125	929	9.74995	unclassified
+reads.pod5	009f5efd-de5d-4a7e-9d17-969c3996cbc8	473bf0edfc2f8f756173de35db5da9b6f6db4959	230	2	171.634	3.27375	171.978	2.93	1230	13.5592	unclassified
+reads.pod5	000a9728-0a7c-4b64-9791-76bb30b63796	473bf0edfc2f8f756173de35db5da9b6f6db4959	105	4	331.319	3.27625	331.59	3.005	1173	11.9264	unclassified
+reads.pod5	00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf	473bf0edfc2f8f756173de35db5da9b6f6db4959	300	3	329.733	2.5165	329.766	2.484	1055	12.888	unclassified
+reads.pod5	0066800d-d191-4833-a495-cfe8b925aca0	473bf0edfc2f8f756173de35db5da9b6f6db4959	56	4	359.11	14.0375	359.35	13.7975	5107	9.07701	unclassified
+reads.pod5	00ad521b-b916-404f-a31d-a657f9aa7756	473bf0edfc2f8f756173de35db5da9b6f6db4959	365	2	566.263	23.6745	566.285	23.652	10974	12.0417	unclassified
+reads.pod5	002f231b-5d37-437f-a027-a2e8b872e73b	473bf0edfc2f8f756173de35db5da9b6f6db4959	118	3	534.745	19.5837	534.949	19.38	8412	9.80529	unclassified
+reads.pod5	005cf7ae-4d74-42dd-ab96-9befed842822	473bf0edfc2f8f756173de35db5da9b6f6db4959	473	2	258.872	29.436	259.165	29.1435	14568	5.17409	unclassified
+reads.pod5	00aeb4ba-e404-49d2-97c5-8fcf22547f81	473bf0edfc2f8f756173de35db5da9b6f6db4959	51	4	297.891	50.1888	297.984	50.0962	19131	8.38011	unclassified
diff --git a/tools/dorado/test-data/dorado.test2.out.tsv b/tools/dorado/test-data/dorado.test2.out.tsv
@@ -0,0 +1,11 @@
+filename	read_id	run_id	channel	mux	start_time	duration	template_start	template_duration	sequence_length_template	mean_qscore_template	barcode
+reads.pod5	00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf	473bf0edfc2f8f756173de35db5da9b6f6db4959	300	3	329.733	2.5165	329.766	2.484	1055	12.888	unclassified
+reads.pod5	0067486b-9f92-4849-8456-671463e64412	473bf0edfc2f8f756173de35db5da9b6f6db4959	84	4	164.018	2.33125	164.249	2.1	884	12.2444	unclassified
+reads.pod5	000a9728-0a7c-4b64-9791-76bb30b63796	473bf0edfc2f8f756173de35db5da9b6f6db4959	105	4	331.319	3.27625	331.59	3.005	1173	11.9264	unclassified
+reads.pod5	0072b26f-f37c-4517-afa7-621543ac2187	473bf0edfc2f8f756173de35db5da9b6f6db4959	317	3	111.275	2.31875	111.492	2.10125	929	9.74995	unclassified
+reads.pod5	009f5efd-de5d-4a7e-9d17-969c3996cbc8	473bf0edfc2f8f756173de35db5da9b6f6db4959	230	2	171.634	3.27375	171.978	2.93	1230	13.5592	unclassified
+reads.pod5	0066800d-d191-4833-a495-cfe8b925aca0	473bf0edfc2f8f756173de35db5da9b6f6db4959	56	4	359.11	14.0375	359.35	13.7975	5107	9.07701	unclassified
+reads.pod5	005cf7ae-4d74-42dd-ab96-9befed842822	473bf0edfc2f8f756173de35db5da9b6f6db4959	473	2	258.872	29.436	259.165	29.1435	14568	5.17409	unclassified
+reads.pod5	002f231b-5d37-437f-a027-a2e8b872e73b	473bf0edfc2f8f756173de35db5da9b6f6db4959	118	3	534.745	19.5837	534.949	19.38	8412	9.80529	unclassified
+reads.pod5	00ad521b-b916-404f-a31d-a657f9aa7756	473bf0edfc2f8f756173de35db5da9b6f6db4959	365	2	566.263	23.6745	566.285	23.652	10974	12.0417	unclassified
+reads.pod5	00aeb4ba-e404-49d2-97c5-8fcf22547f81	473bf0edfc2f8f756173de35db5da9b6f6db4959	51	4	297.891	50.1888	297.984	50.0962	19131	8.38011	unclassified
diff --git a/tools/dorado/test-data/dorado.test3.out.tsv b/tools/dorado/test-data/dorado.test3.out.tsv
@@ -0,0 +1,10 @@
+filename	read_id	run_id	channel	mux	start_time	duration	template_start	template_duration	sequence_length_template	mean_qscore_template	barcode
+reads.pod5	1103e241-dd7f-43bc-ae19-9a3c6326ad83	9bf5b3eb10d3b031970acc022aecad4ecc918865	1560	4	10017.5	0.6548	10017.8	0.354	167	17.5036	SQK-RBK114-96_barcode04
+reads.pod5	11083c69-b52c-454a-be68-fec2a8575a36	9bf5b3eb10d3b031970acc022aecad4ecc918865	2516	4	5861.87	1.81	5861.87	1.808	630	16.7402	unclassified
+reads.pod5	12fb7fac-859b-4990-b818-4713cdfdb7ee	9bf5b3eb10d3b031970acc022aecad4ecc918865	2347	3	9306.98	1.1972	9307.39	0.7776	294	20.0927	SQK-RBK114-96_barcode04
+reads.pod5	131b3680-0768-4d5e-a026-f2bf9b875f99	9bf5b3eb10d3b031970acc022aecad4ecc918865	972	2	9482.91	2.1968	9483.47	1.6404	585	14.6984	unclassified
+reads.pod5	135c81bb-c1eb-4053-8882-62f6bbb15742	9bf5b3eb10d3b031970acc022aecad4ecc918865	1407	2	9193.08	1.358	9193.42	1.0152	432	13.0721	SQK-RBK114-96_barcode01
+reads.pod5	1311ecda-0649-46ad-988d-307a5f4e3bd6	9bf5b3eb10d3b031970acc022aecad4ecc918865	666	2	9861.43	1.7624	9861.77	1.4232	577	17.7034	SQK-RBK114-96_barcode01
+reads.pod5	136e707a-e3eb-44b6-bad7-dcb093db0f76	9bf5b3eb10d3b031970acc022aecad4ecc918865	2219	1	9191.44	2.7884	9192.35	1.8768	716	14.5703	SQK-RBK114-96_barcode01
+reads.pod5	1383d825-29e3-4c83-b0fc-82e35b047122	9bf5b3eb10d3b031970acc022aecad4ecc918865	886	4	6067.83	1.2608	6068.38	0.7152	335	16.3078	unclassified
+reads.pod5	126d5f9f-d665-4ea2-a00a-234c86d88c71	9bf5b3eb10d3b031970acc022aecad4ecc918865	2552	2	7985.15	1.73	7985.71	1.1688	418	19.0671	SQK-RBK114-96_barcode04
diff --git a/tools/dorado/test-data/dorado_pod5_convert.test1.out.pod5 b/tools/dorado/test-data/dorado_pod5_convert.test1.out.pod5