Convert formats - TSI
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Run on GalaxyNote: Deprecated as of May 2025. The mRNA preprocessing previously performed by this workflow is now built into the Fgenesh annotation workflow (881) Version 4. This workflow is no longer needed in the TSI annotation pipeline. Please use workflow 881 Version 4 directly with TransDecoder CDS output from workflow 879 (Extract transcripts).
This is part of a series of workflows to annotate a genome, tagged with TSI-annotation.
These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.
The workflows can be run in this order:
- Repeat masking
- RNAseq QC and read trimming
- Find transcripts
- Combine transcripts
- Extract transcripts
- Convert formats
- Fgenesh annotation
About this workflow:
- Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta
- Runs many steps to convert outputs into the formats required for Fgenesh - .pro, .dat and .cdna
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| transdecoder-nucleotides.fasta | transdecoder-nucleotides.fasta | n/a |
|
| transdecoder-peptides.fasta | transdecoder-peptides.fasta | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | STEP 1 Get IDs for complete, pos transcripts: Grep for lines starting with > | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 3 | grep for lines with complete | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 4 | Remove > from start of lines | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
| 5 | Keep lines that end in (+) | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 6 | STEP 2 | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 7 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 8 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 |
| 9 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 10 | Cut | Cut1 |
| 11 | STEP 3. seqtk subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0 |
| 12 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
| 13 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
| 14 | STEP 4. cut col 1, delimit by pipe | Cut1 |
| 15 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 |
| 16 | seqtk_subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0 |
| 17 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
| 18 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
| 19 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
| 20 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 |
| 21 | STEP 6 Grep headers | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 22 | STEP 9B. grep for > | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 23 | STEP 9A. grep for > | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
| 24 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
| 25 | Sed to remove parentheses | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
| 26 | Cut | Cut1 |
| 27 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 28 | STEP 5 get seq lengths | toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3 |
| 29 | STEP 10A. seqtk seq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/1.4+galaxy0 |
| 30 | awk to extract last field in line | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
| 31 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
| 32 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
| 33 | Cut | Cut1 |
| 34 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
| 35 | Cut | Cut1 |
| 36 | Cut | Cut1 |
| 37 | STEP 7. create chroms file with na lines | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0 |
| 38 | STEP 8. create comments.txt | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0 |
| 39 | paste starts and stops | Paste1 |
| 40 | STEP 9C. paste transcripts and chroms | Paste1 |
| 41 | paste comments and transcript-lengths | Paste1 |
| 42 | STEP 10B. paste starts stops and chroms | Paste1 |
| 43 | Paste | Paste1 |
| 44 | Paste | Paste1 |
| 45 | Paste | Paste1 |
| 46 | Paste | Paste1 |
| 47 | Cut | Cut1 |
| 48 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| output | output | n/a |
|
Version History
v1.1 (latest) Created 17th Apr 2026 at 10:20 by Anna Syme
Fixed disconnected inputs
Frozen
v1.17f29101
Version 1 (earliest) Created 8th May 2024 at 08:23 by Anna Syme
Initial commit
Frozen
Version-1
caf683f
Views: 6203 Downloads: 834 Runs: 2
Created: 8th May 2024 at 08:23
Last updated: 5th May 2026 at 03:28
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Public web page: https://usegalaxy.org.au/
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
This is part of a series of workflows to annotate a genome, tagged with TSI-annotation.
These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.
The workflows can be run in this order:
- Repeat masking
- RNAseq QC and read trimming
- Find transcripts
- Combine transcripts
- Extract transcripts
- Fgenesh annotation
Update May 2026: Note: The "convert formats" workflow (880) is now no longer needed.
