# HG changeset patch
# User iuc
# Date 1773050317 0
# Node ID 36ba1bc79914bd3bc8dbf9fb0fb6d14e5d803b4d
# Parent  2f94e939aef59791279976d65c2c5fa7ce8c86b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt commit f261bcb18c3bb76f0382bb1d7741e48b05bbcb63

diff -r 2f94e939aef5 -r 36ba1bc79914 cutadapt.xml
--- 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." />
diff -r 2f94e939aef5 -r 36ba1bc79914 macros.xml
--- 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>