Ensure correct output formats of seqtk_seq and seqtk_mergefa in all cases #6393
Conversation
- Restricted input formats to only FASTA and compressed FASTA files (.fasta, .fasta.gz). Removed support for FASTQ files. - Updated the tool description and help section to accurately reflect that the tool only merges FASTA files. - Improved the tool's clarity by ensuring it is used for its intended purpose: merging FASTA files only.
Update seqtk_mergefa.xml
"Tool merges FASTA/Q files into a FASTA output and considers the quality threshold for FASTQ files when merging." 1. Clarified the -m option to handle ambiguous bases and conflicts (e.g., N and other IUPAC codes). 2. Improved help documentation with clearer examples and explanations. 3. Refined input parameter labels for better clarity and consistency.
edited echo command line back to #echo
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You need to bump the wrapper version. Maybe just this single one and don't change the macros one. In addition, I think the fasta output of the tool would likely have to be If you have the time, you could also pull in the changes from #6350 and fix the output format there. Very similar issue as yours: the output of that tool should always be fasta or fasta.gz, depending on input compression, but never fastq(.gz). |
seqtk seq actually produces also FASTQ as an output ! |
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yes, I realize. What I wanted to say is that the logic for handling output formats will be similar. |
wm75
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wm75
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FOR CONTRIBUTOR:
Adjust output format when using
-A force FASTA output (discard quality)to FASTA