Mercurial > repos > iuc > ncbi_fcs_gx
changeset 5:2559b7ce2114 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit 14178ea62ed017f16cb0d4ff85fdfdc61dd3b69e
| author | iuc |
|---|---|
| date | Tue, 25 Mar 2025 21:27:03 +0000 (7 days ago) |
| parents | 32d058f3462a |
| children | |
| files | macros.xml ncbi_fcs_gx.xml test-data/output.fcs_gx_report.txt test-data/output.taxonomy.rpt |
| diffstat | 4 files changed, 11 insertions(+), 7 deletions(-) [+] |
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--- a/macros.xml Thu Nov 21 02:20:02 2024 +0000 +++ b/macros.xml Tue Mar 25 21:27:03 2025 +0000 @@ -5,8 +5,8 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.5.4</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">0.5.5</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="biotools"> <xrefs>
--- a/ncbi_fcs_gx.xml Thu Nov 21 02:20:02 2024 +0000 +++ b/ncbi_fcs_gx.xml Tue Mar 25 21:27:03 2025 +0000 @@ -34,9 +34,12 @@ --species '$mode.species' #end if --split-fasta '$mode.screen_adv.split_fasta' - #if $mode.screen_adv.div: + #if $mode.screen_adv.div --div '$mode.screen_adv.div' #end if + #if $mode.screen_adv.ignore_same_kingdom + --ignore-same-kingdom + #end if --gx-db "\${TMPDIR}" --out-basename output --action-report true @@ -111,6 +114,7 @@ </param> <param argument="--split-fasta" type="boolean" checked="true" optional="true" label="Split fasta sequences on N-runs of length at least 10"/> <param argument="--div" type="text" value="" optional="true" label="BLAST-div of the tax-id" help="from 'NCBI BLAST name' on taxon Info page"/> + <param argument="--ignore-same-kingdom" type="boolean" checked="false" optional="true" label="Ignore same-kingdom contamination"/> </section> </when> <when value="clean">
--- a/test-data/output.fcs_gx_report.txt Thu Nov 21 02:20:02 2024 +0000 +++ b/test-data/output.fcs_gx_report.txt Tue Mar 25 21:27:03 2025 +0000 @@ -1,7 +1,7 @@ -##[["FCS genome report", 2, 1], {"git-rev": "v0.5.4-5-g5dfd516", "run-date": "Thu Sep 5 19:38:38 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"}}] +##[["FCS genome report", 2, 1], {"git-rev": "v0.5.5-9-gfc836c1", "run-date": "Tue Mar 25 16:04:25 2025", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.454486, "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 31 Bacteroides salyersiae -JPZV02009577.1 1 600722 600722 EXCLUDE prok:CFB group bacteria 61 Bacteroides bouchesdurhonensis +JPZV02009577.1 1 600722 600722 EXCLUDE prok:CFB group bacteria 61 Bacteroides caecimuris 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 Nov 21 02:20:02 2024 +0000 +++ b/test-data/output.taxonomy.rpt Tue Mar 25 21:27:03 2025 +0000 @@ -1,7 +1,7 @@ -##[["GX taxonomy analysis report", 3, 1], {"git-rev": "v0.5.4-5-g5dfd516", "run-date": "Thu Sep 5 19:38:38 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"}}] +##[["GX taxonomy analysis report", 3, 1], {"git-rev": "v0.5.5-9-gfc836c1", "run-date": "Tue Mar 25 16:04:25 2025", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.454486, "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 +JPZV02009577.1 600722 0,65,0,0,0,0,0 373207 | Bacteroides caecimuris 1796613 prok:CFB group bacteria 373207 125070 743 | 329854 prok:CFB group bacteria 373207 120705 728 | | | 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