Code

Mafft Changes#1337

Code

Merged

bgruening merged 44 commits intobgruening:masterbgruening/galaxytools:masterfrom elischberg:mafftelischberg/galaxytools:mafftCopy head branch name to clipboardMar 20, 2024

+2,692-1,247

Commits

Commits on Nov 6, 2023

• Change help section to better form

  elischberg

  committed
  9d01f21

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• Matched matrix-selection to datatype amino acid

  elischberg

  committed
  2bb2ef5

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• Delete command options in help section

  elischberg

  committed
  3b6df91

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• Fix indentation

  elischberg

  committed
  dc08aac

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• Update version number

  elischberg

  committed
  f85880e

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• Change of datatype selection to a functional form with the appropriate

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  elischberg

  committed
  1e6d3ed

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• Version number correction

  elischberg

  committed
  60b7421

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• Add arguments for matrix-selection of both datatypes

  elischberg

  committed
  6708f28

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• Delete xinsi and qinsi flavours because of missing SCARNA tool for RNA alignments

  elischberg

  committed
  093f309

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• New categorisation of the guidetree-constuction

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  elischberg

  committed
  aa58c46

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• New test-data and sample file for nucleic acid sequence

  elischberg

  committed
  6027e09

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• Mention that default output order is input order

  elischberg

  committed
  7b792bb

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• Fix of fasta3 requiring flavours and original guidetree building flavors

  elischberg

  committed
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Commits on Nov 7, 2023

• Merge branch 'master' into mafft

  elischberg

  committed
  d7ac0f3

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• Fix groupsize parameter

  elischberg

  committed
  98686e9

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• Delete echo of sequence_count

  elischberg

  committed
  a2cfea4

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• Param groupsize fixes

  elischberg

  committed
  f8b0f62

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Commits on Nov 20, 2023

• Add concatenate function in configfile

  elischberg

  committed
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Commits on Nov 21, 2023

• Fix of groupsize param

  elischberg

  committed
  7ed72bd

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• Add tests

  elischberg

  committed
  07db6f0

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• Treeout function failing

  elischberg

  committed
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Commits on Nov 27, 2023

• Fix output tree alignement option

  elischberg

  committed
  b640a2f

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• Setting groupsize standard value to -1 for better handling

  elischberg

  committed
  531bfd8

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• Groupsize param help change

  elischberg

  committed
  6597da2

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• Test fix

  elischberg

  committed
  987643b

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• Create symlinks in workingdir

  elischberg

  committed
  f648282

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• Cosmetic changes

  elischberg

  committed
  1157799

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Commits on Nov 28, 2023

• Change of Test 4

  elischberg

  committed
  b9f83ae

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Commits on Mar 5, 2024

• Update tools/mafft/mafft-add.xml

  bgruening

  authored
  8132c83

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Commits on Mar 11, 2024

• Fix formatting

  wm75

  committed
  f7e4937

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Commits on Mar 12, 2024

• Improve readibility for users and developers

  wm75

  committed
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Commits on Mar 13, 2024

• Disable multithreading during iterative refinement

  wm75

  committed
  7bf9fc3

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• Fix --aamatrix and --fmodel options

  wm75

  committed
  f484936

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• Better presentation & explanation of scoring matrix choices

  wm75

  committed
  f3b3be8

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• Merge pull request #1 from wm75/mafft

  elischberg

  authored
  9c4a975

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• add homepage URL

  bgruening

  authored
  fc78377

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Commits on Mar 14, 2024

• Fix MSA flavour handling and smaller improvements

  wm75

  committed
  5727e22

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Commits on Mar 18, 2024

• Merge pull request #2 from wm75/mafft-more-improvements

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  elischberg

  authored
  e02ad66

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• Fix of Tests

  elischberg

  committed
  a557967

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• Merge branch 'master' into mafft

  elischberg

  authored
  a131279

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Commits on Mar 19, 2024

• Adjust test and add one for mafft --auto

  elischberg

  committed
  4fa198e

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• Merge branch 'master' into mafft

  elischberg

  authored
  f4b7b19

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• Fix tests

  wm75

  committed
  0d0ccff

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• Fix again with all files committed

  wm75

  committed
  fbb0b93

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