# HG changeset patch
# User iuc
# Date 1755266826 0
# Node ID 23f75f8716cfa9d5aafc5e746acaf3b579860bc1
# Parent  8d31d5da86629788bc2d7b022483a865179e4bb7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong commit 5261d1ca6aeb4f7d84769372b1fdad1db59e08b5

diff -r 8d31d5da8662 -r 23f75f8716cf fastplong.xml
--- a/fastplong.xml	Sat Jul 19 08:24:14 2025 +0000
+++ b/fastplong.xml	Fri Aug 15 14:07:06 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT">
+<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
     <description>Filter and trim long reads</description>
     <creator>
         <organization name="Masaryk University" url="https://www.muni.cz/"/>
@@ -6,7 +6,7 @@
     </creator>
     <macros>
         <token name="@TOOL_VERSION@">0.3.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">fastplong</requirement>
@@ -155,12 +155,6 @@
     --cut_front
     --cut_tail
 
-    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_window_size):
-        --cut_window_size $read_mod_options.cutting_by_quality_options.qual_trim.cut_window_size
-    #end if
-    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_mean_quality):
-        --cut_mean_quality $read_mod_options.cutting_by_quality_options.qual_trim.cut_mean_quality
-    #end if
     #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_front_window_size):
         --cut_front_window_size $read_mod_options.cutting_by_quality_options.qual_trim.cut_front_window_size
     #end if
@@ -301,20 +295,18 @@
                     </param>
                     <when value="none"/>
                     <when value="both">
-                        <param argument="--cut_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Cutting window size" help="The size of the sliding window for sliding window trimming, default is 4."/>
-                        <param argument="--cut_mean_quality" type="integer" optional="true" min="1" max="60" value="20" label="Mean quality threshold" help="The bases in the sliding window with mean quality below cutting_quality will be cut, default is 20 (== Q20)."/>
-                        <param argument="--cut_front_window_size" type="integer" optional="true" min="1" max="1000" label="Front window size" help="Override window size for cut_front only. Default: cut_window_size"/>
-                        <param argument="--cut_front_mean_quality" type="integer" optional="true" min="1" max="60" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/>
-                        <param argument="--cut_tail_window_size" type="integer" optional="true" min="1" max="1000" label="Tail window size" help="Override window size for cut_tail only. Default: cut_window_size"/>
-                        <param argument="--cut_tail_mean_quality" type="integer" optional="true" min="1" max="60" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/>
+                        <param argument="--cut_front_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Front window size" help="Override window size for cut_front only. Default: cut_window_size"/>
+                        <param argument="--cut_front_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/>
+                        <param argument="--cut_tail_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Tail window size" help="Override window size for cut_tail only. Default: cut_window_size"/>
+                        <param argument="--cut_tail_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/>
                     </when>
                     <when value="front">
                         <param argument="--cut_front_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Front window size" help="Override window size for cut_front only. Default: cut_window_size"/>
-                        <param argument="--cut_front_mean_quality" type="integer" optional="true" value="20" min="1" max="60" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/>
+                        <param argument="--cut_front_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Front mean quality" help="Override quality threshold for cut_front only. Default: cut_mean_quality"/>
                     </when>
                     <when value="tail">
                         <param argument="--cut_tail_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Tail window size" help="Override window size for cut_tail only. Default: cut_window_size"/>
-                        <param argument="--cut_tail_mean_quality" type="integer" optional="true" value="20" min="1" max="60" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/>
+                        <param argument="--cut_tail_mean_quality" type="integer" optional="true" value="20" min="1" max="36" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/>
                     </when>
                 </conditional>
             </section>
@@ -350,16 +342,30 @@
                 </assert_contents>
             </output>
         </test>
+        
         <test expect_num_outputs="3">
             <param name="in" value="input.fastq"/>
+            <section name="read_mod_options">
+                <section name="cutting_by_quality_options">
+                    <conditional name="qual_trim">
+                        <param name="trim_side" value="both"/>
+                    </conditional>
+                </section>
+            </section>
             <section name="output_options">
                 <param name="report_json" value="true"/>
             </section>
-            <output name="out" file="output.fastq"/>
+            <output name="out" file="quality_cutting_output.fastq"/>
             <output name="report_json">
 				<assert_contents>
 					<has_text text='summary": {'/>
 					<has_text text='fastplong_version": "@TOOL_VERSION@'/>
+					<has_text text="--cut_front"/>
+					<has_text text="--cut_tail"/>
+					<has_text text="--cut_front_window_size 4"/>
+					<has_text text="--cut_front_mean_quality 20"/>
+					<has_text text="--cut_tail_window_size 4"/>
+					<has_text text="--cut_tail_mean_quality 20"/>
 				</assert_contents>
             </output>
         </test>
diff -r 8d31d5da8662 -r 23f75f8716cf test-data/quality_cutting_output.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/quality_cutting_output.fastq	Fri Aug 15 14:07:06 2025 +0000
@@ -0,0 +1,16 @@
+@name
+GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT
++
+EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE
+@name2
+GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT
++
+EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE
+@name3
+GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT
++
+EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE
+@name4
+GCTGCGCATACTTTTCCACGGGGATACTACTGGGTGTTACCGTGGGAATGAATCCTTTTAACCTTAGCAATACGTAAAGGTGCT
++
+EEEEEEEEEEEEEEEEEEEEEEEEE////EEEEEEEEEEEEE////E////EEEEEEEEE///EEEEEEEEEEEEEEEEEEEEE