# HG changeset patch
# User iuc
# Date 1691708272 0
# Node ID 09c589057ee8a056d8b6e6e3ec68e3c592a915dc
# Parent  f8113c25bc6be99ac3d682f457b4b2546c1223d3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4

diff -r f8113c25bc6b -r 09c589057ee8 macros.xml
--- a/macros.xml	Tue Jul 12 15:23:31 2022 +0000
+++ b/macros.xml	Thu Aug 10 22:57:52 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">merqury</xref>
diff -r f8113c25bc6b -r 09c589057ee8 merqury.xml
--- a/merqury.xml	Tue Jul 12 15:23:31 2022 +0000
+++ b/merqury.xml	Thu Aug 10 22:57:52 2023 +0000
@@ -164,6 +164,7 @@
             <option value="stats" selected="true">Stats file</option>
             <option value="bed">BED: hap-mer tracks</option>
             <option value="wig">WIG: hap-mer tracks</option>
+            <option value="hist">Histogram files</option>
             <option value="log">Log file</option>
         </param>
         <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" />
@@ -196,6 +197,10 @@
         <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file">
             <filter>"log" in output_selector</filter>
         </data>
+        <collection name="hist_files" type="list" label="${tool.name} on ${on_string}: histograms">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.hist" format="tabular" directory="output_files"/>
+            <filter>"hist" in output_selector</filter>
+        </collection>
     </outputs>
     <tests>
         <!--Test 01: trio mode-->
@@ -217,7 +222,7 @@
             </output_collection>
         </test>
         <!--Test 02: standard mode with tabular headers -->
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="7">
             <conditional name="mode">
                 <param name="options" value="default"/>
                 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
@@ -227,7 +232,7 @@
                 </conditional>
             </conditional>
             <param name="label" value="output_02"/>
-            <param name="output_selector" value="stats,plots,bed,sizes,qv,wig"/>
+            <param name="output_selector" value="stats,plots,bed,sizes,qv,wig,hist"/>
             <output_collection name="png_files" type="list" count="6">
                 <element name="output_02.assembly.spectra-cn.fl">
                     <assert_contents>
@@ -284,6 +289,12 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output_collection name="hist_files" type="list" count="4">
+                <element name="output_02.spectra-asm" file="output_02.spectra-asm.hist" ftype="tabular"/>
+                <element name="output_02.dist_only" file="output_02.dist_only.hist" ftype="tabular"/>
+                <element name="output_02.assembly.spectra-cn" file="output_02.assembly.spectra-cn.hist" ftype="tabular"/>
+                <element name="output_02.assembly.only" file="output_02.assembly.only.hist" ftype="tabular"/>
+            </output_collection>
         </test>
         <!--Test 03: Standard mode two assemblies-->
         <test expect_num_outputs="2">
diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.assembly.only.hist
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_02.assembly.only.hist	Thu Aug 10 22:57:52 2023 +0000
@@ -0,0 +1,2 @@
+1	0	0
+2	0	0
diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.assembly.spectra-cn.hist
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_02.assembly.spectra-cn.hist	Thu Aug 10 22:57:52 2023 +0000
@@ -0,0 +1,210 @@
+Copies	kmer_multiplicity	Count
+1	1	296
+2	2	381
+3	3	380
+4	4	421
+>4	5	487
+>4	6	531
+>4	7	589
+>4	8	671
+>4	9	705
+>4	10	711
+>4	11	814
+>4	12	733
+>4	13	748
+>4	14	757
+>4	15	737
+>4	16	811
+>4	17	796
+>4	18	784
+>4	19	791
+>4	20	738
+>4	21	738
+>4	22	655
+>4	23	662
+>4	24	648
+>4	25	636
+>4	26	627
+>4	27	592
+>4	28	621
+>4	29	552
+>4	30	542
+>4	31	538
+>4	32	522
+>4	33	514
+>4	34	461
+>4	35	482
+>4	36	449
+>4	37	404
+>4	38	427
+>4	39	429
+>4	40	389
+>4	41	325
+>4	42	354
+>4	43	348
+>4	44	347
+>4	45	325
+>4	46	328
+>4	47	301
+>4	48	273
+>4	49	239
+>4	50	253
+>4	51	259
+>4	52	229
+>4	53	231
+>4	54	219
+>4	55	211
+>4	56	188
+>4	57	189
+>4	58	188
+>4	59	183
+>4	60	174
+>4	61	153
+>4	62	143
+>4	63	152
+>4	64	147
+>4	65	142
+>4	66	157
+>4	67	115
+>4	68	126
+>4	69	104
+>4	70	106
+>4	71	116
+>4	72	106
+>4	73	96
+>4	74	87
+>4	75	99
+>4	76	81
+>4	77	87
+>4	78	78
+>4	79	70
+>4	80	55
+>4	81	56
+>4	82	57
+>4	83	66
+>4	84	59
+>4	85	45
+>4	86	42
+>4	87	40
+>4	88	56
+>4	89	54
+>4	90	44
+>4	91	56
+>4	92	38
+>4	93	44
+>4	94	37
+>4	95	26
+>4	96	33
+>4	97	19
+>4	98	28
+>4	99	27
+>4	100	26
+>4	101	24
+>4	102	32
+>4	103	26
+>4	104	23
+>4	105	24
+>4	106	28
+>4	107	14
+>4	108	20
+>4	109	17
+>4	110	15
+>4	111	16
+>4	112	23
+>4	113	12
+>4	114	20
+>4	115	14
+>4	116	13
+>4	117	10
+>4	118	8
+>4	119	8
+>4	120	9
+>4	121	11
+>4	122	7
+>4	123	14
+>4	124	8
+>4	125	7
+>4	126	10
+>4	127	5
+>4	128	8
+>4	129	8
+>4	130	10
+>4	131	9
+>4	132	9
+>4	133	6
+>4	134	7
+>4	135	3
+>4	136	8
+>4	137	4
+>4	138	7
+>4	139	2
+>4	140	5
+>4	141	3
+>4	142	9
+>4	143	9
+>4	144	4
+>4	145	4
+>4	146	3
+>4	147	2
+>4	148	2
+>4	149	3
+>4	150	4
+>4	151	3
+>4	152	1
+>4	153	1
+>4	154	5
+>4	155	1
+>4	156	4
+>4	157	2
+>4	158	1
+>4	159	2
+>4	160	6
+>4	161	3
+>4	164	1
+>4	165	3
+>4	166	2
+>4	167	1
+>4	168	3
+>4	169	4
+>4	170	1
+>4	171	1
+>4	172	4
+>4	173	2
+>4	174	1
+>4	175	1
+>4	176	1
+>4	177	1
+>4	178	1
+>4	179	1
+>4	182	1
+>4	184	2
+>4	186	4
+>4	187	1
+>4	188	1
+>4	190	1
+>4	192	1
+>4	196	1
+>4	197	1
+>4	198	2
+>4	199	1
+>4	200	1
+>4	201	1
+>4	202	2
+>4	205	1
+>4	206	2
+>4	210	1
+>4	213	1
+>4	218	1
+>4	219	1
+>4	224	1
+>4	225	1
+>4	227	1
+>4	231	1
+>4	242	1
+>4	262	1
+>4	268	1
+>4	271	1
+>4	276	1
+>4	298	1
+>4	304	1
+>4	321	1
diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.dist_only.hist
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_02.dist_only.hist	Thu Aug 10 22:57:52 2023 +0000
@@ -0,0 +1,1 @@
+assembly	0	0
diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.spectra-asm.hist
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_02.spectra-asm.hist	Thu Aug 10 22:57:52 2023 +0000
@@ -0,0 +1,210 @@
+Assembly	kmer_multiplicity	Count
+assembly	1	296
+assembly	2	381
+assembly	3	380
+assembly	4	421
+assembly	5	487
+assembly	6	531
+assembly	7	589
+assembly	8	671
+assembly	9	705
+assembly	10	711
+assembly	11	814
+assembly	12	733
+assembly	13	748
+assembly	14	757
+assembly	15	737
+assembly	16	811
+assembly	17	796
+assembly	18	784
+assembly	19	791
+assembly	20	738
+assembly	21	738
+assembly	22	655
+assembly	23	662
+assembly	24	648
+assembly	25	636
+assembly	26	627
+assembly	27	592
+assembly	28	621
+assembly	29	552
+assembly	30	542
+assembly	31	538
+assembly	32	522
+assembly	33	514
+assembly	34	461
+assembly	35	482
+assembly	36	449
+assembly	37	404
+assembly	38	427
+assembly	39	429
+assembly	40	389
+assembly	41	325
+assembly	42	354
+assembly	43	348
+assembly	44	347
+assembly	45	325
+assembly	46	328
+assembly	47	301
+assembly	48	273
+assembly	49	239
+assembly	50	253
+assembly	51	259
+assembly	52	229
+assembly	53	231
+assembly	54	219
+assembly	55	211
+assembly	56	188
+assembly	57	189
+assembly	58	188
+assembly	59	183
+assembly	60	174
+assembly	61	153
+assembly	62	143
+assembly	63	152
+assembly	64	147
+assembly	65	142
+assembly	66	157
+assembly	67	115
+assembly	68	126
+assembly	69	104
+assembly	70	106
+assembly	71	116
+assembly	72	106
+assembly	73	96
+assembly	74	87
+assembly	75	99
+assembly	76	81
+assembly	77	87
+assembly	78	78
+assembly	79	70
+assembly	80	55
+assembly	81	56
+assembly	82	57
+assembly	83	66
+assembly	84	59
+assembly	85	45
+assembly	86	42
+assembly	87	40
+assembly	88	56
+assembly	89	54
+assembly	90	44
+assembly	91	56
+assembly	92	38
+assembly	93	44
+assembly	94	37
+assembly	95	26
+assembly	96	33
+assembly	97	19
+assembly	98	28
+assembly	99	27
+assembly	100	26
+assembly	101	24
+assembly	102	32
+assembly	103	26
+assembly	104	23
+assembly	105	24
+assembly	106	28
+assembly	107	14
+assembly	108	20
+assembly	109	17
+assembly	110	15
+assembly	111	16
+assembly	112	23
+assembly	113	12
+assembly	114	20
+assembly	115	14
+assembly	116	13
+assembly	117	10
+assembly	118	8
+assembly	119	8
+assembly	120	9
+assembly	121	11
+assembly	122	7
+assembly	123	14
+assembly	124	8
+assembly	125	7
+assembly	126	10
+assembly	127	5
+assembly	128	8
+assembly	129	8
+assembly	130	10
+assembly	131	9
+assembly	132	9
+assembly	133	6
+assembly	134	7
+assembly	135	3
+assembly	136	8
+assembly	137	4
+assembly	138	7
+assembly	139	2
+assembly	140	5
+assembly	141	3
+assembly	142	9
+assembly	143	9
+assembly	144	4
+assembly	145	4
+assembly	146	3
+assembly	147	2
+assembly	148	2
+assembly	149	3
+assembly	150	4
+assembly	151	3
+assembly	152	1
+assembly	153	1
+assembly	154	5
+assembly	155	1
+assembly	156	4
+assembly	157	2
+assembly	158	1
+assembly	159	2
+assembly	160	6
+assembly	161	3
+assembly	164	1
+assembly	165	3
+assembly	166	2
+assembly	167	1
+assembly	168	3
+assembly	169	4
+assembly	170	1
+assembly	171	1
+assembly	172	4
+assembly	173	2
+assembly	174	1
+assembly	175	1
+assembly	176	1
+assembly	177	1
+assembly	178	1
+assembly	179	1
+assembly	182	1
+assembly	184	2
+assembly	186	4
+assembly	187	1
+assembly	188	1
+assembly	190	1
+assembly	192	1
+assembly	196	1
+assembly	197	1
+assembly	198	2
+assembly	199	1
+assembly	200	1
+assembly	201	1
+assembly	202	2
+assembly	205	1
+assembly	206	2
+assembly	210	1
+assembly	213	1
+assembly	218	1
+assembly	219	1
+assembly	224	1
+assembly	225	1
+assembly	227	1
+assembly	231	1
+assembly	242	1
+assembly	262	1
+assembly	268	1
+assembly	271	1
+assembly	276	1
+assembly	298	1
+assembly	304	1
+assembly	321	1