Mercurial > repos > lparsons > cutadapt
changeset 32:36ba1bc79914 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt commit f261bcb18c3bb76f0382bb1d7741e48b05bbcb63
| author | iuc |
|---|---|
| date | Mon, 09 Mar 2026 09:58:37 +0000 |
| parents | 2f94e939aef5 |
| children | |
| files | cutadapt.xml macros.xml |
| diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/cutadapt.xml Fri Feb 27 19:24:16 2026 +0000 +++ b/cutadapt.xml Mon Mar 09 09:58:37 2026 +0000 @@ -352,7 +352,8 @@ <section name="filter_options" title="Read Filtering Options"> <param argument="--discard-trimmed" type="boolean" checked="false" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" /> <param argument="--discard_untrimmed" type="boolean" checked="false" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." /> - <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum length (R1)" help="Discard reads that, after processing, are shorter than LENGTH. Note: You can set this parameter to zero to keep empty reads (with zero-length sequence and quality string) in the output, but some downstream tools may have problems with these. Default: 0" /> + <!-- the following param's default value is intentionally set to 1 and different from the commandline tool's 0 to avoid hard to debug issues with downstream tools --> + <param argument="--minimum-length" type="integer" min="0" value="1" label="Minimum length (R1)" help="Discard reads that, after processing, are shorter than LENGTH. Note: You can set this parameter to zero to keep empty reads (with zero-length sequence and quality string) in the output, but some downstream tools may have problems with these. Default: 1" /> <param name="minimum_length2" type="integer" min="0" value="" optional="true" label="Minimum length (R2)" help="For paired-end data, you can specify here a separate minimum length cutoff to apply to R2 reads. Leave empty to reuse the R1 cutoff set above. Ignored for single-end data." /> <param argument="--maximum-length" type="integer" min="0" optional="true" value="" label="Maximum length (R1)" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded." /> <param name="maximum_length2" type="integer" min="0" value="" optional="true" label="Maximum length (R2)" help="For paired-end data, you can specify here a separate maximum length cutoff to apply to R2 reads. Leave empty to reuse the R1 cutoff set above. Ignored for single-end data." />
--- a/macros.xml Fri Feb 27 19:24:16 2026 +0000 +++ b/macros.xml Mon Mar 09 09:58:37 2026 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">5.2</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token> <xml name="edam_ontology"> <edam_topics>