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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit 7f32f58df93f5c295eeacbb4367ec91ed7463dad |
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modified:
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 |
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| diff -r 49f8eae39606 -r c228e49365c4 macros.xml --- a/macros.xml Thu May 30 10:49:36 2024 +0000 +++ b/macros.xml Fri Aug 23 20:55:07 2024 +0000 |
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| @@ -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"> |
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| diff -r 49f8eae39606 -r c228e49365c4 test-data/output.clean.fa.gz |
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| Binary file test-data/output.clean.fa.gz has changed |
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| diff -r 49f8eae39606 -r c228e49365c4 test-data/output.contam.fa.gz |
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| Binary file test-data/output.contam.fa.gz has changed |
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| diff -r 49f8eae39606 -r c228e49365c4 test-data/output.fcs_gx_report.txt --- 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 |
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| @@ -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 |
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| diff -r 49f8eae39606 -r c228e49365c4 test-data/output.taxonomy.rpt --- 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 |
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| @@ -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 |