changeset 3:e6fc152a2462 draft default tip

Uploaded
author greg
date Tue, 28 Mar 2023 14:17:59 +0000
parents 66c368ee50fe
children
files p_chunks.xml test-data/input.blastdbn test-data/input.psl test-data/output.tsv
diffstat 4 files changed, 3023 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/p_chunks.xml	Thu Jan 26 16:24:22 2023 +0000
+++ b/p_chunks.xml	Tue Mar 28 14:17:59 2023 +0000
@@ -29,7 +29,11 @@
         <data name="output_plasmids" format="tsv" label="${tool.name} on ${on_string} (plasmids)"/>
     </outputs>
     <tests>
-        <!-- Tests are not possible due to file size requirements -->
+        <test>
+            <param name="plasmid_psl" value="input.psl" ftype="psl"/>
+            <param name="plasmid_database" value="input.blastdbn" ftype="blastdbn"/>
+            <output name="output_plasmids" value="output.tsv" ftype="tsv"/>
+        </test>
     </tests>
     <help>
 **What it does**
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.blastdbn	Tue Mar 28 14:17:59 2023 +0000
@@ -0,0 +1,11 @@
+
+
+Building a new DB, current time: 01/09/2023 14:25:15
+New DB name:   /home/galaxies/lrn/jwd/000/609/working/dataset_1038_files/blastdb
+New DB title:  BLAST of Plasmids and Vectors
+Sequence type: Nucleotide
+Keep MBits: T
+Maximum file size: 1000000000B
+Adding sequences from FASTA; added 34305 sequences in 17.7537 seconds.
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.psl	Tue Mar 28 14:17:59 2023 +0000
@@ -0,0 +1,3005 @@
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+1530	5	0	0	4	5	5	7	-	NC_020239.1	76490	72497	74032	contig_2	181626	90	1627	10	4,37,122,2,1238,3,96,1,9,18,	72497,72501,72538,72660,72664,73902,73906,74003,74005,74014,	90,95,133,257,259,1498,1501,1597,1598,1609,
+1530	5	0	0	4	5	5	7	-	NC_020249.1	77351	57435	58970	contig_2	181626	90	1627	10	4,37,122,2,1238,3,96,1,9,18,	57435,57439,57476,57598,57602,58840,58844,58941,58943,58952,	90,95,133,257,259,1498,1501,1597,1598,1609,
+1530	5	0	0	4	5	5	7	-	CP004071.1	76490	72497	74032	contig_2	181626	90	1627	10	4,37,122,2,1238,3,96,1,9,18,	72497,72501,72538,72660,72664,73902,73906,74003,74005,74014,	90,95,133,257,259,1498,1501,1597,1598,1609,
+1530	5	0	0	4	5	5	7	-	CP004070.1	77351	57435	58970	contig_2	181626	90	1627	10	4,37,122,2,1238,3,96,1,9,18,	57435,57439,57476,57598,57602,58840,58844,58941,58943,58952,	90,95,133,257,259,1498,1501,1597,1598,1609,
+1525	5	0	0	4	5	10	12	-	CP020757.1	85218	23171	24701	contig_2	181626	90	1627	15	4,37,6,115,2,429,83,73,650,3,77,18,1,9,18,	23171,23175,23212,23218,23333,23337,23766,23849,23922,24572,24576,24653,24672,24674,24683,	90,95,133,140,257,259,689,773,847,1498,1501,1579,1597,1598,1609,
+1530	5	0	0	4	5	5	7	-	NZ_CP021065.1	86488	46975	48510	contig_2	181626	90	1627	10	4,37,122,2,1238,3,96,1,9,18,	46975,46979,47016,47138,47142,48380,48384,48481,48483,48492,	90,95,133,257,259,1498,1501,1597,1598,1609,
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+6890	818	0	0	37	818	95	1998	-	CP004876.1	299843	168293	176001	contig_2	181626	155094	163982	133	11,26,2,4,1,3,3,5,5,2047,5,20,7,195,4,21,3,74,134,274,6,2,196,5,169,7,269,7,542,10,8,1,7,5,3,7,19,6,2,6,2,17,9,5,6,9,6,1,4,7,4,2,6,17,5,5,4,3,10,4,17,7,2,18,2,3,4,4,4,7,6,11,3,2,7,5,2,4,5,7,4,2,4,10,3,2,6,13,16,5,6,26,4,11,4,3,5,2,10,13,6,4,4,2,5,2,9,7,3,12,3,4,14,9,5,7,7,3,4,6,7,1293,3,158,35,4,258,2,8,2,44,4,440,	168293,168305,168331,168335,168339,168340,168344,168348,168354,168359,170406,170412,170432,170440,170637,170641,170664,170667,170742,170876,171156,171162,171164,171361,171366,171538,172252,172521,172529,173071,173082,173090,173091,173098,173103,173106,173113,173132,173138,173142,173148,173150,173169,173178,173185,173191,173200,173206,173207,173211,173219,173223,173225,173231,173249,173254,173259,173266,173269,173279,173283,173300,173307,173309,173327,173329,173332,173336,173342,173346,173353,173359,173370,173373,173375,173382,173388,173390,173394,173399,173406,173410,173412,173416,173426,173430,173432,173440,173453,173470,173475,173481,173507,173511,173522,173526,173529,173534,173536,173546,173559,173565,173569,173573,173575,173580,173582,173591,173598,173601,173613,173617,173621,173635,173644,173650,173657,173667,173670,173676,173683,173690,174985,174988,175198,175233,175238,175500,175503,175511,175513,175557,175561,	155094,155105,155132,155134,155139,155141,155144,155147,155152,155159,157207,157212,157233,157240,157435,157441,157462,157467,157541,157676,157950,157961,157964,158160,158166,158335,158342,158612,158619,159164,159174,159186,159190,159202,159210,159214,159352,159374,159381,159383,159390,159393,159410,159420,159425,159432,159445,159458,159461,159472,159479,159493,159497,159509,159526,159535,159541,159545,159551,159563,159654,159673,159695,159698,159717,159722,159726,159766,159770,159775,159783,159791,159804,159808,159812,159822,159827,159831,159837,159898,159906,159913,159916,159922,159936,159939,159942,159948,160538,160554,160563,160570,160598,160604,160912,160917,160924,160931,160935,160946,160965,160974,160979,160987,160997,161006,161010,161511,161523,161532,161546,161549,161556,161669,161679,161684,161693,161700,161704,161708,161714,161722,163015,163020,163178,163214,163218,163476,163478,163487,163490,163537,163542,
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+2301	56	0	0	4	56	3	5	-	CP000228.1	239246	226566	228923	contig_2	181626	161676	163982	8	12,6,9,47,2,1420,331,474,	226566,226578,226585,226594,226643,226645,228117,228449,	161676,161689,161695,161706,161753,161757,163177,163508,
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+2882	6	0	0	5	6	12	15	+	DQ889678.1	272145	15593	18481	contig_2	181626	163982	166879	18	113,916,230,6,22,11,833,62,128,1,58,176,5,125,3,113,2,78,	15593,15706,16622,16853,16859,16881,16893,17726,17788,17918,17919,17977,18153,18158,18283,18287,18401,18403,	163982,164096,165015,165245,165252,165275,165286,166121,166184,166312,166314,166373,166550,166556,166682,166685,166798,166801,
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+2882	6	0	0	5	6	12	15	+	NC_010924.1	270082	10559	13447	contig_2	181626	163982	166879	18	113,916,230,6,22,11,833,62,128,1,58,176,5,125,3,113,2,78,	10559,10672,11588,11819,11825,11847,11859,12692,12754,12884,12885,12943,13119,13124,13249,13253,13367,13369,	163982,164096,165015,165245,165252,165275,165286,166121,166184,166312,166314,166373,166550,166556,166682,166685,166798,166801,
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+918	0	0	0	0	0	1	1	-	AAEN01000030.1	95646	33495	34413	contig_2	181626	180064	180983	2	728,190,	33495,34223,	180064,180793,
+540	1	0	0	1	1	3	13	-	NZ_CP009636.1	238933	42329	42870	contig_2	181626	180435	180988	5	105,17,3,233,182,	42329,42434,42452,42455,42688,	180435,180541,180558,180562,180806,
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+540	1	0	0	1	1	3	13	-	ABDM02000063.1	238933	113649	114190	contig_2	181626	180435	180988	5	105,17,3,233,182,	113649,113754,113772,113775,114008,	180435,180541,180558,180562,180806,
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+492	12	0	0	8	12	7	10	-	CP009649.1	140953	65388	65892	contig_2	181626	181035	181537	16	26,2,3,10,169,8,18,53,3,25,2,119,3,15,7,29,	65388,65415,65417,65420,65431,65600,65608,65629,65685,65688,65713,65716,65835,65839,65855,65863,	181035,181061,181064,181068,181078,181248,181258,181276,181329,181335,181361,181363,181483,181486,181501,181508,
+511	7	0	0	2	7	1	1	+	NZ_AP014867.1	130548	30505	31023	contig_2	181626	181114	181626	4	382,5,65,59,	30505,30893,30899,30964,	181114,181496,181501,181567,
+511	7	0	0	2	7	1	1	+	AP014867.1	130548	30505	31023	contig_2	181626	181114	181626	4	382,5,65,59,	30505,30893,30899,30964,	181114,181496,181501,181567,
+425	0	0	0	0	0	0	0	-	NC_020385.1	328151	46032	46457	contig_2	181626	181114	181539	1	425,	46032,	181114,
+425	0	0	0	0	0	0	0	-	CP004137.1	328151	46032	46457	contig_2	181626	181114	181539	1	425,	46032,	181114,
+509	1	0	0	1	1	1	1	+	NC_017199.1	139013	104667	105177	contig_2	181626	181116	181626	3	392,58,59,	104667,105060,105118,	181116,181508,181567,
+509	1	0	0	1	1	1	1	+	CP002510.1	139013	104667	105177	contig_2	181626	181116	181626	3	392,58,59,	104667,105060,105118,	181116,181508,181567,
+353	0	0	0	0	0	1	1	-	NZ_LDKD02000006.1	40312	27899	28252	contig_2	181626	181272	181626	2	294,59,	27899,28193,	181272,181567,
+353	0	0	0	0	0	1	1	-	LDKD02000006.1	40312	27899	28252	contig_2	181626	181272	181626	2	294,59,	27899,28193,	181272,181567,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tsv	Tue Mar 28 14:17:59 2023 +0000
@@ -0,0 +1,2 @@
+query.name	plasmid.name	plasmid.accession	query.size	aligned.bases	plasmid.size	plasmid.missing
+contig_2	Bacillus anthracis str. Sterne plasmid pXO1	CP009540.1	181626	181626	181624	0