From 9ec830a98da45d5fb2f92a817c7cd0376504be90 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Sat, 27 Nov 2021 10:45:45 +0100
Subject: [PATCH] cutadapt: add missing arguments and remove unsued test params
 (#4195)

* cutadapt: remove absent read_modification

this was once the select of a conditional which was removed in
https://github.com/galaxyproject/tools-iuc/commit/9a3d1b1c3c2e2d1f6d06fa92e9a95580e8529291

* same for output_filtering

* add missing arguments to command

--strip-suffix seems absent from the beginning
--discard-cassava was apparently forgotten in https://github.com/galaxyproject/tools-iuc/pull/3704

xref https://github.com/galaxyproject/tools-iuc/issues/4095
---
 tools/cutadapt/cutadapt.xml | 10 ++++------
 tools/cutadapt/macros.xml   |  2 +-
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
index 7b7b6a09713..fa795b546fa 100644
--- a/tools/cutadapt/cutadapt.xml
+++ b/tools/cutadapt/cutadapt.xml
@@ -134,7 +134,7 @@ $filter_options.discard_untrimmed
 #if str($filter_options.max_expected_errors):
     --max-expected-errors=$filter_options.max_expected_errors
 #end if
-
+$filter_options.discard_cassava
 
 #if str($read_mod_options.quality_cutoff) != '0':
    --quality-cutoff=$read_mod_options.quality_cutoff
@@ -143,6 +143,9 @@ $filter_options.discard_untrimmed
     --nextseq-trim=$read_mod_options.nextseq_trim
 #end if
 $read_mod_options.trim_n
+#if $read_mod_options.strip_suffix != ''
+    --strip-suffix $read_mod_options.strip_suffix
+#end if
 #if str($read_mod_options.shorten_options.shorten_values) == 'True':
     #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
         --length=$read_mod_options.shorten_options.length
@@ -505,11 +508,9 @@ $read_mod_options.zero_cap
                     </conditional>
                 </repeat>
             </section>
-            <param name="output_filtering" value="filter"/>
             <section name="filter_options">
                 <param name="discard_trimmed" value="True"/>
             </section>
-            <param name="read_modification" value="none"/>
             <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
             <assert_command>
                 <has_text text="--discard-trimmed"/>
@@ -526,8 +527,6 @@ $read_mod_options.zero_cap
                     </conditional>
                 </repeat>
             </section>
-            <param name="output_filtering" value="default"/>
-            <param name="read_modification" value="none"/>
             <param name="output_selector" value="rest_file,json_stats"/>
             <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
             <output name="json_stats" file="cutadapt_rest.json" ftype="json"/>
@@ -545,7 +544,6 @@ $read_mod_options.zero_cap
                     </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"/>
         </test>
diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml
index 567d23a28a2..4507b02ea54 100644
--- a/tools/cutadapt/macros.xml
+++ b/tools/cutadapt/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token>
     <xml name="edam_ontology">
         <edam_topics>