Mercurial > repos > p.lucas > bt_typer
changeset 7:af97e0ff67c0 draft
Uploaded
| author | p.lucas |
|---|---|
| date | Thu, 28 Mar 2024 11:26:42 +0000 |
| parents | b9a5f0f56606 |
| children | 56b5f6dd6dee |
| files | Bt_detect_galaxy_wrapper.xml |
| diffstat | 1 files changed, 45 insertions(+), 40 deletions(-) [+] |
line wrap: on
line diff
--- a/Bt_detect_galaxy_wrapper.xml Thu Mar 28 11:01:24 2024 +0000 +++ b/Bt_detect_galaxy_wrapper.xml Thu Mar 28 11:26:42 2024 +0000 @@ -43,53 +43,58 @@ </outputs> <help> <![CDATA[ - Tool obtained form github: https://github.com/afelten-Anses/Bt_typing/ + +Tool obtained form github: https://github.com/afelten-Anses/Bt_typing/ - Bacillus thuringiensis serovars aizaiwai and kurstaki detection from blastx output. +Bacillus thuringiensis serovars aizaiwai and kurstaki detection from blastx output. - If you want to use your own detection table, file is configured like this (tabular separator): +If you want to use your own detection table, file is configured like this (tabular separator): + +----- - X header lines corresponding to the marker - (name list of reference) - \#\#\# - ==================== ========== ========== ========= === - .. serovars A serovars B Cluster 1 ... - ==================== ========== ========== ========= === - complete name 0 -1 1 0 - ==================== ========== ========== ========= === +| X header lines corresponding to the marker +| (name list of reference) +| ### - +================ ========== ========== ========= === +.. serovars A serovars B Cluster 1 ... +================ ========== ========== ========= === +complete name 0 -1 1 0 +================ ========== ========== ========= === - X header lines corresponding to the marker - (name list of reference) - ### (mandatory) - Table with the association between serovar and marker - (column header: "empty header" serovars A serovars B Cluster 1 ...) - (line example: "complete name" 0 -1 1 0...) +----- + +Example with the default file: + +----- - Example with the default file: +| Bt WP_021728236.1|Bt_CwlA WP_000237488.1|Bt_intQ WP_000858032.1|Bt_group_3916 WP_042596929.1|Bt_group_20749 WP_002101540.1|Bt_group_20361 WP_000998670.1|Bt_sdpR +| aizaiwai WP_021728520.1|Bta_apr +| kurstaki WP_003273526.1|Btk_group_27293 WP_001293418.1|Btk_group_27336 +| clusterA WP_000415284.1|clustera_group_10114 +| clusterB WP_050062578.1|clusterb_rapF WP_131256056.1|clusterb_group_20667 +| clusterC AHZ54004.1|clusterc_lexA +| clusterD WP_000791073.1|clusterd_clpP1 +| ### - Bt WP_021728236.1|Bt_CwlA WP_000237488.1|Bt_intQ WP_000858032.1|Bt_group_3916 WP_042596929.1|Bt_group_20749 WP_002101540.1|Bt_group_20361 WP_000998670.1|Bt_sdpR - aizaiwai WP_021728520.1|Bta_apr - kurstaki WP_003273526.1|Btk_group_27293 WP_001293418.1|Btk_group_27336 - clusterA WP_000415284.1|clustera_group_10114 - clusterB WP_050062578.1|clusterb_rapF WP_131256056.1|clusterb_group_20667 - clusterC AHZ54004.1|clusterc_lexA - clusterD WP_000791073.1|clusterd_clpP1 - ### - Bt aizaiwai kurstaki clusterA clusterB clusterC clusterD - Bacillus thuringiensis 1 -1 -1 0 0 0 0 - Bacillus thuringiensis 1 1 1 0 0 0 0 - not Bacillus thuringiensis -1 0 0 0 0 0 0 - Bacillus thuringiensis aizaiwai not clustered 1 1 -1 -1 -1 0 0 - Bacillus thuringiensis aizaiwai not clustered 1 1 -1 1 1 0 0 - Bacillus thuringiensis kurstaki not clustered 1 -1 1 0 0 -1 -1 - Bacillus thuringiensis kurstaki not clustered 1 -1 1 0 0 1 1 - Bacillus thuringiensis aizaiwai cluster A 1 1 -1 1 -1 0 0 - Bacillus thuringiensis aizaiwai cluster B 1 1 -1 -1 1 0 0 - Bacillus thuringiensis kurstaki cluster C 1 -1 1 0 0 1 -1 - Bacillus thuringiensis kurstaki cluster D 1 -1 1 0 0 -1 1 - +============================================= ==== ========== ======== ======== ======== ======== ======== +.. Bt aizaiwai kurstaki clusterA clusterB clusterC clusterD +--------------------------------------------- ---- ---------- -------- -------- -------- -------- -------- +Bacillus thuringiensis 1 -1 -1 0 0 0 0 +Bacillus thuringiensis 1 1 1 0 0 0 0 +not Bacillus thuringiensis -1 0 0 0 0 0 0 +Bacillus thuringiensis aizaiwai not clustered 1 1 -1 -1 -1 0 0 +Bacillus thuringiensis aizaiwai not clustered 1 1 -1 1 1 0 0 +Bacillus thuringiensis kurstaki not clustered 1 -1 1 0 0 -1 -1 +Bacillus thuringiensis kurstaki not clustered 1 -1 1 0 0 1 1 +Bacillus thuringiensis aizaiwai cluster A 1 1 -1 1 -1 0 0 +Bacillus thuringiensis aizaiwai cluster B 1 1 -1 -1 1 0 0 +Bacillus thuringiensis kurstaki cluster C 1 -1 1 0 0 1 -1 +Bacillus thuringiensis kurstaki cluster D 1 -1 1 0 0 -1 1 +============================================= ==== ========== ======== ======== ======== ======== ======== + +----- + ]]> </help> </tool>