hyphy/capheine-core-and-compare

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Workflow Type: Galaxy

Runs CAPHEINE selection analyses with optional foreground/background branch labeling for branch comparisons.

SEEK ID: https://workflowhub.eu/workflows/2111?version=2

Inputs

ID Name Description Type
foreground list (optional) foreground list (optional) File containing list of foreground sequence names (one per line). Leave empty to skip foreground sequence selection.
  • File?
foreground regexp (optional) foreground regexp (optional) Regular expression to match foreground sequence names for branch labeling.
  • string?
reference Fasta reference Fasta genome fasta for reference assembly to use to identify cds
  • File
reference GTF reference GTF gtf for reference assembly to use to identify cds
  • File
unaligned sequences unaligned sequences unaligned sequences
  • File[]

Steps

ID Name Description
5 HyPhy: Core n/a
6 Save RegEx to File Save RegEx to File toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3
7 Collect Sequence Identifiers Collect Sequence Identifiers Grep1
8 Clean RegEx This step makes sure the regex is whitespace-trimmed, blank lines are dropped, and anything outside [0-9A-Za-z_] becomes _ to match HyPhy CLN behavior. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
9 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
10 Count characters in RegEx Count characters in RegEx wc_gnu
11 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy3
12 Check is RegEx Empty Check is RegEx Empty toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
13 Trim trimmer
14 (Boolean) Continue Foreground Sequence List Creation (Boolean) Continue Foreground Sequence List Creation param_value_from_file
15 Build Foreground Sequence List from RegEx Build Foreground Sequence List from RegEx Grep1
16 Choose Foreground Sequences Choose Foreground Sequences toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
17 Count foreground sequences This counts the number of lines in the provided list of foreground sequences. If the count is > 0 RELAX and Contrast-FEL will also run. wc_gnu
18 Check non-zero foreground list This will return 'true' if the count of foreground sequences is > 0 and 'false' otherwise toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
19 (Boolean) Continue foreground comparison (Boolean) Continue foreground comparison param_value_from_file
20 HyPhy: Compare Subworkflow step
21 DRHIP toolshed.g2.bx.psu.edu/repos/iuc/drhip/drhip/0.1.4+galaxy0

Outputs

ID Name Description Type
combined_sites combined_sites n/a
  • File
combined_comparison_summary combined_comparison_summary n/a
  • File
combined_comparison_site combined_comparison_site n/a
  • File
combined_summary combined_summary n/a
  • File

Version History

v0.2 (latest) Created 5th Jul 2026 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 06be2cc

v0.1 (earliest) Created 13th Mar 2026 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 1ca4700
help Creators and Submitter
Creators
  • Danielle Callan
  • Hannah Verdonk
  • Sergei L. Kosakovsky Pond
Submitter
License
MIT License (MIT)
Activity

Views: 772   Downloads: 3490   Runs: 0

Created: 13th Mar 2026 at 03:01

Annotated Properties
Scientific disciplines
Computer Science
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