# HG changeset patch
# User iuc
# Date 1724680065 0
# Node ID 0a355925c1bf7f3a91f0ed946e9a4df7338297b0
# Parent  e42205a5495e64fd4cb3b3e0fe066c0666dbd797
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67

diff -r e42205a5495e -r 0a355925c1bf adapter_removal.xml
--- a/adapter_removal.xml	Wed May 04 13:45:22 2022 +0000
+++ b/adapter_removal.xml	Mon Aug 26 13:47:45 2024 +0000
@@ -50,6 +50,8 @@
 --qualitybase '33'
 --qualitybase-output '33'
 --qualitymax $fastq_options.qualitymax
+$fastq_options.convert_uracils
+$fastq_options.mask_degenerate_bases
 
 ###### FASTQ Trimming Options
 --adapter1 '$fastq_trimming_options.adapter1'
@@ -143,6 +145,8 @@
         <!-- FASTQ Options -->
         <section name="fastq_options" title="FASTQ Options" expanded="false">
             <param argument="--qualitymax" type="integer" value="41" min="0" max="93" label="Maximum Phred score expected in input files and used when writing output files" help="Possible values are 0 to 93 for Phred+33 encoded files"/>
+            <param argument="--mask-degenerate-bases" type="boolean" truevalue="--mask-degenerate-bases" falsevalue="" checked="false" label="Mask degenerate/ambiguous bases (B/D/H/K/M/N/R/S/V/W/Y)" help="This option will replace 'N's; if this option is not used, AdapterRemoval will abort upon encountering degenerate bases."/>
+            <param argument="--convert-uracils" type="boolean" truevalue="--convert-uracils" falsevalue="" checked="false" label="Convert uracils (U) to thymine (T) " help="If this option is not used, AdapterRemoval will abort upon encountering uracils."/>
         </section>
         <!-- FASTQ Trimming Options -->
         <section name="fastq_trimming_options" title="FASTQ Trimming Options" expanded="false">
@@ -265,6 +269,10 @@
             <param name="input_type" value="pair"/>
             <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
             <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
+            <section name="fastq_options">
+                <param name="convert_uracils" value="false"/>
+                <param name="mask_degenerate_bases" value="true"/>
+            </section>
             <output name="output_settings" ftype="txt">
                 <assert_contents>
                     <has_size value="2594" delta="10"/>
diff -r e42205a5495e -r 0a355925c1bf macros.xml
--- a/macros.xml	Wed May 04 13:45:22 2022 +0000
+++ b/macros.xml	Mon Aug 26 13:47:45 2024 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.3.3</token>
+    <token name="@TOOL_VERSION@">2.3.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.09</token>
     <token name="@DATATYPES@">fastqsanger.gz,fastqsanger</token>