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add ChewBBACA #5899
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add ChewBBACA #5899
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0d90128
add ChewBBACA
nilchia e31b5f9
update macros
nilchia 9c403c7
add compare by sim_size for zip files
nilchia 1c22e19
3rd tool PrepExternalSchema
nilchia b38e5c7
Change to min value of --l
nilchia f1b2d85
Add PrepExternalSchema tool from chewbbaca
nilchia d22ff0c
Some minor adjustment to xmls. create output of allelecall in test-data
nilchia 87386a9
update test-data
nilchia 22e2901
update test-data
nilchia 698b1fd
add prepareexternalschema
nilchia cbc4c70
removing uploaded wrong files
nilchia 5b94ea1
aading DownloadSchema tool
nilchia cef81ad
aading DownloadSchema tool
nilchia 7468524
Add AlleleCallEvaluator
nilchia 933f5fd
update alleleCallEvaluator
nilchia b7dc7c0
Add FastTree requirement to macros
nilchia 67a7f4c
add AlleleCallEvaluator
nilchia ad1b55a
update AlleleCall.xml to write cds_coordinates as output
nilchia 0256df7
Update AllelCallEvluator
nilchia 0ca96db
update test.data
nilchia 1092358
update test-data
nilchia 0bd6e4f
add ExtractCgMLST.xml
nilchia 58bd441
Merge branch 'galaxyproject:main' into chewbbaca
nilchia 422a8a2
add NSStats.xml
nilchia 9d1dc78
add JoinProfiles.xml
nilchia d867846
updata test-data
nilchia 7fe39d5
final NSStats.xml
nilchia d67b1b7
Final NSStats.xml with help
nilchia 2a34a6a
final DownloadSchema.xml
nilchia c97a0c0
final DownloadSchema with help and a little correction to NSStema.xml
nilchia 15007cd
final CreatSchema.xml with help
nilchia 2d5f915
final PrepExternalSchema.xml with help
nilchia 49804ed
Final AlleleCall.xml with help
nilchia dec0a57
NSStats.xml reviewed
nilchia fcfc806
macros updated species_id
nilchia e5ed80e
revised CreateSchenma
nilchia d2fab38
revised CreateSchema with another test
nilchia 4a280ba
revised AlleleCall.xml
nilchia c871034
revised AlleleCallEvaluator.xml
nilchia 85b2a0d
revised DownloadSchema
nilchia cdfd121
revised ExtractCgMLST.xml
nilchia 91a8efb
updated macros - INPUT as token
nilchia 56a4bcb
Revised PrepExternalSchema.xml
nilchia 44e8331
revised Joinprofile.xml
nilchia 5c66c2c
Added --cds_input
nilchia 08efc33
Added --cds_input
nilchia a7a4520
Added --cds-input
nilchia ca1f086
Added --cds-input
nilchia 5b4a0b7
Added --genes-list
nilchia f39fec1
added --common
nilchia dd62428
update test-data
nilchia cf924b0
Merge branch 'galaxyproject:main' into chewbbaca
nilchia e06d66e
updated test of DownloadSchema.xml
nilchia b5d53ff
updated test-data
nilchia 559ae10
updated test-data
nilchia 3ff7677
update on test and output of ExtractCgMLST.xml
nilchia 8008177
Update tools/chewbbaca/AlleleCall.xml
nilchia 5f5f261
Update tools/chewbbaca/AlleleCall.xml
nilchia d7650b9
Update tools/chewbbaca/AlleleCall.xml
nilchia e1199b1
Update tools/chewbbaca/PrepExternalSchema.xml
nilchia 533811b
Update tools/chewbbaca/AlleleCallEvaluator.xml
nilchia 9c534c8
added test for 3 optional outputs of AllelCall.xml
nilchia 9bb69d2
Update command line of JoinProfiles.xml
nilchia fd52c6e
corrected id of tools all lowercase with chewbbaca prefix
nilchia 2173b85
corrected if statement for optional file
nilchia e50e9c6
change some params to multiple select type
nilchia 4718a0d
added '' to all files and directories
nilchia c6acc9c
added '' to all files and directories
nilchia 01170b2
better name for macros tokens
nilchia 855121f
the result of AlleleCallEvluator is now a collection
nilchia eabe306
help is edited
nilchia edce444
the output is now an html file not a collection
nilchia fcca0f8
corrected output filtering in AlleleCall.xml
nilchia 5dca753
update test-data
nilchia bcf0d83
--cds-input is boolean now
nilchia e011a57
added a test for --cds in CreateSchema.xml
nilchia 93c7722
update test data
nilchia b7a76b9
--cds is boolean for AlleleCall.xml
nilchia 6203ca7
added test for annotation file in AlleleCallEvaluator.xml
nilchia 788e640
updateed help for AlleleCall.xml ExtractCgMLST.xml
nilchia 1c51e77
update the name of test2 output
nilchia 28219f5
update on 2nd test of AlleleCallEvaluator
nilchia 4b45c8f
Update tools/chewbbaca/CreateSchema.xml
nilchia b669c99
changed test of CreateSchema to check the archive members
nilchia 1772a31
changed test of DownloadSchema to check the archive members
nilchia 4be4711
changed format=tsv to =tabular in CreateSchema
nilchia a0e8b31
changed format=tsv to =tabular in JoinProfile
nilchia 0f0cc2d
compare diff in JoinProfile
nilchia c50ca26
compare diff in AlleleCallEvaluator
nilchia 3a94dc7
compare diff and assert_contents in NSSTATS
nilchia 72259d6
test checks archive members in PrepExternalSchema
nilchia 52195a5
sim_size to diff in AlleleCall
nilchia 9224590
deleted unnecessary test data
nilchia 2a8c54c
update test check in NSSTAT
nilchia 969e98b
update test data
nilchia bfd3a5d
updated test for NSSTATS. line_diff
nilchia dcda29d
Update line_diff
nilchia e306bfb
update line_diff
nilchia 47ed2ac
update on NSSTATS test
nilchia 3810705
Merge branch 'galaxyproject:main' into chewbbaca
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -8,7 +8,7 @@ Contacts: [email protected] | |
| ======================= | ||
| chewBBACA - NSStats | ||
| ======================= | ||
| Started at: 2024-04-03T10:24:19 | ||
| Started at: 2024-04-11T17:01:56 | ||
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||
| Retrieving data... | ||
|
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@@ -35,5 +35,5 @@ Clostridium neonatale 16 1 2350 13115 | |
| ------------------------------------------------------------------------------ | ||
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| Finished at: 2024-04-03T10:24:23 | ||
| Finished at: 2024-04-11T17:02:00 | ||
| Took 0m 4s. | ||
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updating the time will not help much, if you have time in your diffs ... you need to allow for certain lines of difference with
lines_difftools-iuc/tools/lofreq/lofreq_filter.xml
Line 210 in 26fe7d2
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Thanks.
I added
line_diff="4"and it passed the planemo test but here it got error, I putassert_contentsfor the test.