# HG changeset patch
# User iuc
# Date 1625260817 0
# Node ID 6985f04c1585c5a6848d5cad2ac2c6456d59d22b
# Parent  0a6402ed2416c2f1a9f284673dbe455cc450ee57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"

diff -r 0a6402ed2416 -r 6985f04c1585 cutadapt.xml
--- a/cutadapt.xml	Wed Jun 02 22:46:52 2021 +0000
+++ b/cutadapt.xml	Fri Jul 02 21:20:17 2021 +0000
@@ -149,9 +149,6 @@
 #if str($read_mod_options.length_tag) != '':
     --length-tag='$read_mod_options.length_tag'
 #end if
-#if str($read_mod_options.cut) != '0':
-    --cut=$read_mod_options.cut
-#end if
 #if str($read_mod_options.rename) != '':
     --rename='$read_mod_options.rename'
 #end if
@@ -237,7 +234,7 @@
                 </when>
                 <when value="False">
                 </when>
-            </conditional>   
+            </conditional>
             <param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
             <param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
                 <option value="any" selected="True">Any: a read pair is discarded (or redirected) if one of the reads (R1 or R2) fulfills the filtering criterion. </option>
@@ -300,7 +297,6 @@
                 </sanitizer>
                 <validator type="regex">[A-Za-z0-9 {}=_]+</validator>
             </param>
-            <param argument="--cut" label="Remove a fixed number of bases" type="integer" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
             <param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
         </section>
 
@@ -388,16 +384,28 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
         </test>
         <!-- Ensure single end fastq.gz works -->
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
         </test>
         <!-- Ensure paired end fastq.gz works -->
@@ -405,10 +413,22 @@
             <param name="type" value="paired" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
             <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source2">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
             <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
             <assert_command>
@@ -429,10 +449,22 @@
                     <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
                 </collection>
             </param>
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source2">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <output_collection name="out_pairs" type="paired">
                 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
                 <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
@@ -442,15 +474,27 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="builtin"/>
-            <param name="adapter" value="TGTAGGCC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="builtin"/>
+                        <param name="adapter" value="TGTAGGCC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
         </test>
         <!-- Ensure discard file output works -->
         <test expect_num_outputs="1">
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="TTAGACATATCTCCGTCG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="TTAGACATATCTCCGTCG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <param name="output_filtering" value="filter"/>
             <section name="filter_options">
                 <param name="discard_trimmed" value="True"/>
@@ -464,8 +508,14 @@
         <!-- Ensure rest file output works -->
         <test expect_num_outputs="2">
             <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AAAGATG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AAAGATG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <param name="output_filtering" value="default"/>
             <param name="read_modification" value="none"/>
             <param name="output_selector" value="rest_file"/>
@@ -476,8 +526,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <param name="read_modification" value="modify"/>
             <param name="nextseq_trim" value="20" />
             <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
@@ -486,8 +542,14 @@
         <test expect_num_outputs="3">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <param name="output_selector" value="report,info_file" />
             <output name="out1" value="cutadapt_small.out" ftype="fastq"/>
             <output name="report">
@@ -559,8 +621,14 @@
         <test expect_num_outputs="2">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AAAT"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AAAT"/>
+                    </conditional>
+                </repeat>
+            </section>
             <param name="output_selector" value="untrimmed_file" />
             <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
             <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
@@ -569,11 +637,17 @@
         <test expect_num_outputs="2">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <param name="output_selector" value="untrimmed_file" />
             <output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/>
-            <!-- 
+            <!--
                 Do not use the decompress option for this assertion, since it does NOT test that the file is compressed
                 See discussion at https://github.com/galaxyproject/galaxy/issues/7671
                 `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the
@@ -586,10 +660,22 @@
             <param name="type" value="paired" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
             <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="filter_options">
                 <param name="discard_untrimmed" value="true"/>
                 <param name="minimun_length" value="1"/>
@@ -608,9 +694,13 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-             <section name="read_mod_options">
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
                 <param name="cut" value="5"/>
             </section>
             <output name="out1" file="cutadapt_small_cut.out" ftype="fastq"/>
@@ -619,10 +709,16 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+                <param name="cut" value="5"/>
+            </section>
             <section name="read_mod_options">
-                <param name="cut" value="5"/>
                 <param name="rename" value="{id} barcode={cut_prefix}"/>
             </section>
             <output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
@@ -635,8 +731,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="CGTCCGAANTAG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="CGTCCGAANTAG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="action" value="retain"/>
             </section>
@@ -645,8 +747,14 @@
            <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="CGTCCGAANTAG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="CGTCCGAANTAG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="action" value="mask"/>
             </section>
@@ -655,8 +763,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="CGTCCGAANTAG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="CGTCCGAANTAG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="action" value="lowercase"/>
             </section>
@@ -665,8 +779,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="CGTCCGAANTAG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="CGTCCGAANTAG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="action" value="none"/>
             </section>
@@ -676,8 +796,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="TAAACAGATTAGT"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="TAAACAGATTAGT"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="revcomp" value="true"/>
             </section>
@@ -688,10 +814,22 @@
             <param name="type" value="paired" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
             <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="ATCTGGTTCC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="CTACAAG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="ATCTGGTTCC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source2">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="CTACAAG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="filter_options">
                 <param name="minimum_length" value="30"/>
                 <param name="pair_filter" value="both"/>
@@ -712,10 +850,22 @@
             <param name="type" value="paired" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
             <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source2">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="filter_options">
                 <param name="pair_filter" value="both"/>
                 <param name="maximum_length" value="50"/>
@@ -736,10 +886,22 @@
             <param name="type" value="paired" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
             <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source2">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="filter_options">
                 <param name="pair_filter" value="both"/>
                 <param name="minimum_length" value="10"/>
@@ -761,10 +923,22 @@
             <param name="type" value="paired" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
             <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source2">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="filter_options">
                 <param name="pair_filter" value="both"/>
                 <param name="minimum_length" value="10"/>
@@ -786,8 +960,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGCCGCTANGACG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGCCGCTANGACG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="read_mod_options">
                 <conditional name="shorten_options">
                     <param name="shorten_values" value="True"/>
@@ -800,8 +980,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGCCGCTANGACG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGCCGCTANGACG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="read_mod_options">
                 <conditional name="shorten_options">
                     <param name="shorten_values" value="True"/>
@@ -815,8 +1001,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGCGGCTTAGACG"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGCGGCTTAGACG"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="filter_options">
                 <param name="max_expected_errors" value="10"/>
             </section>
@@ -826,8 +1018,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="GAANTAGCTACCAC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="GAANTAGCTACCAC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="internal" value="X"/>
             </section>
@@ -840,10 +1038,22 @@
             <param name="type" value="paired" />
             <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
             <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
-            <param name="adapter_source_list" value="user"/>
-            <param name="adapter" value="AGATCGGAAGAGC"/>
-            <param name="adapter_source_list2" value="user"/>
-            <param name="adapter2" value="AGATCGGAAGAGC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source2">
+                        <param name="adapter_source_list2" value="user"/>
+                        <param name="adapter2" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="internal" value="X"/>
             </section>
@@ -856,8 +1066,14 @@
         <test expect_num_outputs="1">
             <param name="type" value="single" />
             <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
-            <param name="adapter_source_list" value="builtin"/>
-            <param name="adapter" value="TGTAGGCC"/>
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="builtin"/>
+                        <param name="adapter" value="TGTAGGCC"/>
+                    </conditional>
+                </repeat>
+            </section>
             <section name="adapter_options">
                 <param name="internal" value="X"/>
             </section>
diff -r 0a6402ed2416 -r 6985f04c1585 macros.xml
--- a/macros.xml	Wed Jun 02 22:46:52 2021 +0000
+++ b/macros.xml	Fri Jul 02 21:20:17 2021 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.4</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy1</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0632</edam_topic>
@@ -265,7 +265,7 @@
                     </conditional>
                 </repeat>
 
-                <param name="cut" argument="-u" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." />
+                <param name="cut" argument="--cut" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." />
 
             </section>