Mercurial > repos > iuc > ncbi_fcs_gx

changeset 2:c228e49365c4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit 7f32f58df93f5c295eeacbb4367ec91ed7463dad
author iuc
date Fri, 23 Aug 2024 20:55:07 +0000
parents 49f8eae39606
children ed1ef564da41
files macros.xml test-data/output.clean.fa.gz test-data/output.contam.fa.gz test-data/output.fcs_gx_report.txt test-data/output.taxonomy.rpt
diffstat 5 files changed, 15 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu May 30 10:49:36 2024 +0000
+++ b/macros.xml	Fri Aug 23 20:55:07 2024 +0000
@@ -5,7 +5,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.5.0</token>
+    <token name="@TOOL_VERSION@">0.5.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="biotools">
Binary file test-data/output.clean.fa.gz has changed
Binary file test-data/output.contam.fa.gz has changed
--- a/test-data/output.fcs_gx_report.txt	Thu May 30 10:49:36 2024 +0000
+++ b/test-data/output.fcs_gx_report.txt	Fri Aug 23 20:55:07 2024 +0000
@@ -1,7 +1,7 @@
-##[["FCS genome report", 2, 1], {"git-rev": "+branch--", "run-date": "Wed Jan 10 08:58:52 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.358706, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"]}}]
+##[["FCS genome report", 2, 1], {"git-rev": "v0.5.4-5-g5dfd516", "run-date": "Fri Aug 23 19:21:28 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.455294, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"], "genome-hash": "dbb3380351f70e9b"}}]
 #seq_id	start_pos	end_pos	seq_len	action	div	agg_cont_cov	top_tax_name
-JPZV02005859.1	1	705930	705930	REVIEW	prok:CFB group bacteria	22	Bacteroides xylanisolvens
-JPZV02009577.1	1	600722	600722	EXCLUDE	prok:CFB group bacteria	52	Bacteroides caecimuris
-JPZV02016362.1	1	432265	432265	EXCLUDE	prok:CFB group bacteria	45	Bacteroides salyersiae
-JPZV02031416.1	1	170387	170387	REVIEW	prok:CFB group bacteria	18	Bacteroides sp. CBA7301
-JPZV02034235.1	1	131158	131158	REVIEW	prok:CFB group bacteria	24	Bacteroides faecichinchillae
+JPZV02005859.1	1	705930	705930	REVIEW	prok:CFB group bacteria	31	Bacteroides salyersiae
+JPZV02009577.1	1	600722	600722	EXCLUDE	prok:CFB group bacteria	61	Bacteroides bouchesdurhonensis
+JPZV02016362.1	1	432265	432265	EXCLUDE	prok:CFB group bacteria	54	Bacteroides caecimuris
+JPZV02031416.1	1	170387	170387	REVIEW	prok:CFB group bacteria	28	Bacteroides caecimuris
+JPZV02034235.1	1	131158	131158	EXCLUDE	prok:CFB group bacteria	38	Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223
--- a/test-data/output.taxonomy.rpt	Thu May 30 10:49:36 2024 +0000
+++ b/test-data/output.taxonomy.rpt	Fri Aug 23 20:55:07 2024 +0000
@@ -1,8 +1,8 @@
-##[["GX taxonomy analysis report", 3, 1], {"git-rev": "+branch--", "run-date": "Wed Jan 10 08:58:52 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.358706, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"]}}]
-#seq-id	seq-len	(xp,lc,co,n,xc)-len	cvg-by-all	sep1	tax-name-1	tax-id-1	div-1	cvg-by-div-1	cvg-by-tax-1	score-1	sep2	tax-id-2	div-2	cvg-by-div-2	cvg-by-tax-2	score-2	sep3	tax-id-3	div-3	cvg-by-div-3	cvg-by-tax-3	score-3	sep4	tax-id-4	div-4	cvg-by-div-4	cvg-by-tax-4	score-4	sep5	reserved	result	div	div_pct_cvg
-JPZV02005859.1	705930	0,1139,0,0,0	159470	|	Bacteroides xylanisolvens	371601	prok:CFB group bacteria	159470	49227	393	|	1796613	prok:CFB group bacteria	159470	48051	387	|						|						|	n/a	low-coverage	prok:CFB group bacteria	23
-JPZV02009577.1	600722	0,65,0,0,0	316464	|	Bacteroides caecimuris	1796613	prok:CFB group bacteria	316464	137645	782	|	371601	prok:CFB group bacteria	316464	120328	757	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	53
-JPZV02016362.1	432265	0,0,0,0,0	197253	|	Bacteroides salyersiae	291644	prok:CFB group bacteria	197253	74527	520	|	246787	prok:CFB group bacteria	197253	74971	512	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	46
-JPZV02031416.1	170387	0,60,0,0,0	32395	|	Bacteroides sp. CBA7301	2715212	prok:CFB group bacteria	32395	13706	205	|	1297750	prok:CFB group bacteria	32395	12253	201	|						|						|	n/a	low-coverage	prok:CFB group bacteria	19
-JPZV02034235.1	131158	0,0,0,0,0	33221	|	Bacteroides faecichinchillae	871325	prok:CFB group bacteria	33221	17243	230	|	1121098	prok:CFB group bacteria	33221	15138	222	|						|						|	n/a	low-coverage	prok:CFB group bacteria	25
-JPZV02046037.1	26753	0,0,0,0,0	2720	|	Bacteroides graminisolvens DSM 19988 = JCM 15093	1121097	prok:CFB group bacteria	2720	912	45	|	28111	prok:CFB group bacteria	2720	821	45	|						|						|	n/a	low-coverage	prok:CFB group bacteria	10
+##[["GX taxonomy analysis report", 3, 1], {"git-rev": "v0.5.4-5-g5dfd516", "run-date": "Fri Aug 23 19:21:28 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.455294, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"], "genome-hash": "dbb3380351f70e9b"}}]
+#seq-id	seq-len	(xp,lc,co,n,mt,pt,pm)-len	cvg-by-all	sep1	tax-name-1	tax-id-1	div-1	cvg-by-div-1	cvg-by-tax-1	score-1	sep2	tax-id-2	div-2	cvg-by-div-2	cvg-by-tax-2	score-2	sep3	tax-id-3	div-3	cvg-by-div-3	cvg-by-tax-3	score-3	sep4	tax-id-4	div-4	cvg-by-div-4	cvg-by-tax-4	score-4	sep5	reserved	result	div	div_pct_cvg
+JPZV02005859.1	705930	0,1139,0,0,0,0,0	227139	|	Bacteroides salyersiae	291644	prok:CFB group bacteria	227139	47267	364	|	1796613	prok:CFB group bacteria	227139	40278	342	|						|						|	n/a	low-coverage	prok:CFB group bacteria	32
+JPZV02009577.1	600722	0,65,0,0,0,0,0	374876	|	Bacteroides bouchesdurhonensis	1841855	prok:CFB group bacteria	374876	122690	746	|	1796613	prok:CFB group bacteria	374876	125102	742	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	62
+JPZV02016362.1	432265	0,0,0,0,0,0,0	238387	|	Bacteroides caecimuris	1796613	prok:CFB group bacteria	238387	78677	508	|	1852362	prok:CFB group bacteria	238387	76183	487	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	55
+JPZV02031416.1	170387	0,60,0,0,0,0,0	48647	|	Bacteroides caecimuris	1796613	prok:CFB group bacteria	48647	16469	208	|	435590	prok:CFB group bacteria	48647	15004	201	|						|						|	n/a	low-coverage	prok:CFB group bacteria	29
+JPZV02034235.1	131158	0,0,0,0,0,0,0	50739	|	Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223	1121098	prok:CFB group bacteria	50739	27281	262	|	871325	prok:CFB group bacteria	50739	19889	228	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	39
+JPZV02046037.1	26753	0,0,0,0,0,0,0	1402	|	Bacteroides eggerthii	28111	prok:CFB group bacteria	1402	1258	50	|	1121096	prok:CFB group bacteria	1402	803	42	|						|						|	n/a	low-coverage	prok:CFB group bacteria	5