# HG changeset patch
# User iuc
# Date 1752913454 0
# Node ID 8d31d5da86629788bc2d7b022483a865179e4bb7
# Parent  1d34936d44970f48295cc266dfbc92018e4c30e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong commit 8ff99077479b995d644277bacb038478f870409f

diff -r 1d34936d4497 -r 8d31d5da8662 fastplong.xml
--- a/fastplong.xml	Mon Jun 02 10:09:14 2025 +0000
+++ b/fastplong.xml	Sat Jul 19 08:24:14 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy0" profile="23.2" license="MIT">
+<tool id="fastplong" name="Fastplong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="MIT">
     <description>Filter and trim long reads</description>
     <creator>
         <organization name="Masaryk University" url="https://www.muni.cz/"/>
@@ -6,163 +6,430 @@
     </creator>
     <macros>
         <token name="@TOOL_VERSION@">0.3.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">fastplong</requirement>
     </requirements>
     <command detect_errors="exit_code">
-        <![CDATA[
-        fastplong 
-        --thread \${GALAXY_SLOTS:-1}
-        --report_title 'fastplong report for $in'
-        --in '$in'
-        --out '$output'
-        #if $reads_to_process: 
-            --reads_to_process '$reads_to_process'
-        #end if
-        $disable_quality_filtering
-        $disable_adapter_trimming
-        #if $start_adapter:
-            --start_adapter '$start_adapter'
-        #end if
-        #if $end_adapter:
-            --end_adapter '$end_adapter'
-        #end if
-        #if $adapter_fasta:
-            --adapter_fasta '$adapter_fasta'
-        #end if
-        #if $distance_threshold:
-            --distance_threshold '$distance_threshold'
-        #end if
-        #if $trimming_extension:
-            --trimming_extension '$trimming_extension'
-        #end if
-        #if $trim_front:
-            --trim_front '$trim_front'
-        #end if
-        #if $trim_tail:
-            --trim_tail '$trim_tail'
-        #end if
-        $trim_poly_x
-        #if $poly_x_min_len:
-            --poly_x_min_len '$poly_x_min_len'
-        #end if
-        $cut_front
-        $cut_tail
-        #if $cut_window_size:
-            --cut_window_size '$cut_window_size'
-        #end if
-        #if $cut_mean_quality:
-            --cut_mean_quality '$cut_mean_quality'
-        #end if
-        #if $cut_front_window_size:
-            --cut_front_window_size '$cut_front_window_size'
-        #end if
-        #if $cut_front_mean_quality:
-            --cut_front_mean_quality '$cut_front_mean_quality'
-        #end if
-        #if $cut_tail_window_size:
-            --cut_tail_window_size '$cut_tail_window_size'
-        #end if
-        #if $cut_tail_mean_quality:
-            --cut_tail_mean_quality '$cut_tail_mean_quality'
-        #end if
-        #if $qualified_quality_phred:
-            --qualified_quality_phred '$qualified_quality_phred'
-        #end if
-        #if $unqualified_percent_limit:
-            --unqualified_percent_limit '$unqualified_percent_limit'
-        #end if
-        #if $n_base_limit:
-            --n_base_limit '$n_base_limit'
-        #end if
-        #if $mean_qual:
-            --mean_qual '$mean_qual'
-        #end if
-        $disable_length_filtering:
-        #if $length_required:
-            --length_required '$length_required'
-        #end if
-        #if $length_limit:
-            --length_limit '$length_limit'
-        #end if
-        $low_complexity_filter:
-        #if $complexity_threshold:
-            --complexity_threshold '$complexity_threshold'
-        #end if
-        $failed_out failed_reads.fastq
-        ]]>
+ <![CDATA[
+ #import re
+
+ ## Link input files
+
+ #set ext = '.fastq'
+
+ #if $in.is_of_type('fastq.gz')
+    #set ext = '.fastq.gz'
+ #end if
+
+ #set $in_name = re.sub('[^\w\-\s]', '_', str($in.element_identifier)) + $ext
+ ln -sf '$in' '$in_name' &&
+
+ ## Run fastplong
+ fastplong 
+ 
+ --thread \${GALAXY_SLOTS:-1}
+ --report_title 'fastplong report for $in_name'
+ --in '$in_name'
+ --out long${ext}
+
+ #if $reads_to_process: 
+    --reads_to_process '$reads_to_process'
+ #end if
+
+ ## Adapter Trimming Options
+ 
+ #if $adapter_trimming_options.adapter_trim.disable_adapter_trimming == 'yes'
+    --disable_adapter_trimming
+ #else
+
+   #if str($adapter_trimming_options.adapter_trim.start_adapter):
+     --start_adapter '$adapter_trimming_options.adapter_trim.start_adapter'
+   #end if
+
+   #if str($adapter_trimming_options.adapter_trim.end_adapter):
+     --end_adapter '$adapter_trimming_options.adapter_trim.end_adapter'
+   #end if
+
+   #if $adapter_trimming_options.adapter_trim.adapter_fasta:
+     --adapter_fasta '$adapter_trimming_options.adapter_fasta'
+   #end if
+
+   --distance_threshold $adapter_trimming_options.adapter_trim.distance_threshold
+   --trimming_extension $adapter_trimming_options.adapter_trim.trimming_extension
+ #end if
+
+ ## Global Trimming Options
+
+ #if str($global_trimming_options.trim_front):
+     --trim_front $global_trimming_options.trim_front
+ #end if
+
+ #if str($global_trimming_options.trim_tail):
+     --trim_tail $global_trimming_options.trim_tail
+ #end if
+
+
+ ## Filter Options
+
+ ## Quality filtering options
+
+ #if $filter_options.quality_filtering_options.qual_filt.disable_quality_filtering == 'yes'
+   --disable_quality_filtering
+ #else
+
+   #if str($filter_options.quality_filtering_options.qual_filt.qualified_quality_phred):
+     --qualified_quality_phred $filter_options.quality_filtering_options.qual_filt.qualified_quality_phred
+   #end if
+   #if str($filter_options.quality_filtering_options.qual_filt.unqualified_percent_limit):
+     --unqualified_percent_limit $filter_options.quality_filtering_options.qual_filt.unqualified_percent_limit
+   #end if
+   #if str($filter_options.quality_filtering_options.qual_filt.n_base_limit):
+     --n_base_limit $filter_options.quality_filtering_options.qual_filt.n_base_limit
+   #end if
+   #if str($filter_options.quality_filtering_options.qual_filt.mean_qual):
+     --mean_qual $filter_options.quality_filtering_options.qual_filt.mean_qual
+   #end if
+ #end if
+
+ ## Length filtering options
+
+ #if $filter_options.length_filtering_options.len_filt.disable_length_filtering == 'yes'
+   --disable_length_filtering 
+ #else
+   #if str($filter_options.length_filtering_options.len_filt.length_required):
+     --length_required $filter_options.length_filtering_options.len_filt.length_required
+   #end if
+
+   #if str($filter_options.length_filtering_options.len_filt.length_limit):
+     --length_limit $filter_options.length_filtering_options.len_filt.length_limit
+   #end if
+ #end if
+
+ ## Low complexity filtering options
+
+ #if $filter_options.low_complexity_filter.compl_filt.low_complexity_filter == 'yes'
+   --low_complexity_filter
+
+   #if str($filter_options.low_complexity_filter.compl_filt.complexity_threshold):
+     --complexity_threshold $filter_options.low_complexity_filter.compl_filt.complexity_threshold
+   #end if
+ #end if
+
+ ## Read Modification Options
+
+ ### PolyX tail trimming
+
+ #if $read_mod_options.polyx_tail_trimming.polyx.trim_poly_x == 'yes'
+    --trim_poly_x
+    #if $read_mod_options.polyx_tail_trimming.polyx.poly_x_min_len
+       --poly_x_min_len $read_mod_options.polyx_tail_trimming.polyx.poly_x_min_len
+    #end if
+ #end if
+
+ ### Per read cutting by quality options
+
+ #if $read_mod_options.cutting_by_quality_options.qual_trim.trim_side == 'front'
+	--cut_front
+
+    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_front_window_size):
+        --cut_front_window_size $read_mod_options.cutting_by_quality_options.qual_trim.cut_front_window_size
+    #end if
+    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_front_mean_quality):
+        --cut_front_mean_quality $read_mod_options.cutting_by_quality_options.qual_trim.cut_front_mean_quality
+    #end if
+
+ #else if $read_mod_options.cutting_by_quality_options.qual_trim.trim_side == 'tail'
+    --cut_tail
+
+    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_window_size):
+        --cut_tail_window_size $read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_window_size
+    #end if
+    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_mean_quality):
+        --cut_tail_mean_quality $read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_mean_quality
+    #end if
+
+
+ #else if $read_mod_options.cutting_by_quality_options.qual_trim.trim_side == 'both'
+    --cut_front
+    --cut_tail
+
+    #if str($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 $read_mod_options.cutting_by_quality_options.qual_trim.cut_front_window_size
+    #end if
+    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_front_mean_quality):
+        --cut_front_mean_quality $read_mod_options.cutting_by_quality_options.qual_trim.cut_front_mean_quality
+    #end if
+    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_window_size):
+        --cut_tail_window_size $read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_window_size
+    #end if
+    #if str($read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_mean_quality):
+        --cut_tail_mean_quality $read_mod_options.cutting_by_quality_options.qual_trim.cut_tail_mean_quality
+    #end if
+
+ #end if
+
+ #if str($output_options.failed_out):
+    $output_options.failed_out failed_reads.fastq
+ #end if
+
+ &&
+ mv long${ext} '${out}'
+
+  ]]>
     </command>
     <inputs>
-        <param argument="--in" type="data" format="fastq,fastq.gz" label="Input FASTQ file"/>
+        <param argument="--in" type="data" format="fastq,fastq.gz" label="Input Long Reads" help="Input FASTQ file with long reads"/>
         <param argument="--reads_to_process" type="integer" optional="true" label="Number of reads to process" help="Limit the number of reads to process. Useful for quick QC or creating subsets."/>
-        <param argument="--disable_quality_filtering" type="boolean" truevalue="--disable_quality_filtering" falsevalue="" checked="false" label="Disable quality filtering?" help="By default, quality filtering is enabled. Enable this option to turn it off."/>
-        <param argument="--disable_adapter_trimming" type="boolean" truevalue="--disable_adapter_trimming" falsevalue="" checked="false" label="Disable adapter trimming?" help="By default, adapter trimming is enabled. Enable this option to turn it off."/>
-        <param argument="--start_adapter" type="text" optional="true" label="Start adapter sequence (5')" help="Specify the adapter sequence at the 5' end of reads. Leave blank to auto-detect."/>
-        <param argument="--end_adapter" type="text" optional="true" label="End adapter sequence (3')" help="Specify the adapter sequence at the 3' end of reads. Leave blank to auto-detect."/>
-        <param argument="--adapter_fasta" type="data" format="fasta" optional="true" label="Adapter sequences (FASTA file)" help="Specify a FASTA file with adapter sequences to trim."/>
-        <param argument="--distance_threshold" type="float" min="0" max="1" optional="true" label="Adapter distance threshold" help="Threshold of adapter-length. Range: 0.0–1.0"/>
-        <param argument="--trimming_extension" type="integer" optional="true" label="Trimming extension length" help="Extend trimming beyond the adapter match to clean up the sequence more thoroughly. Default is 10"/>
-        <param argument="--trim_front" type="integer" optional="true" label="Trim front (5') bases" help="Trim this many bases from the start (5') of each read. Default: 0"/>
-        <param argument="--trim_tail" type="integer" optional="true" label="Trim tail (3') bases" help="Trim this many bases from the end (3') of each read. Default: 0"/>
-        <param argument="--trim_poly_x" type="boolean" truevalue="--trim_poly_x" falsevalue="" checked="false" label="Trim polyX tails?" help="Enable to trim polyX stretches at the 3' end."/>
-        <param argument="--poly_x_min_len" type="integer" optional="true" label="Minimum polyX length" help="Minimum length to detect polyX in the tail. Default: 10"/>
-        <param argument="--cut_front" type="boolean" truevalue="--cut_front" falsevalue="" checked="false" label="Enable sliding-window trimming from 5' end?" help="Trim from 5' end until window mean quality is above threshold."/>
-        <param argument="--cut_tail" type="boolean" truevalue="--cut_tail" falsevalue="" checked="false" label="Enable sliding-window trimming from 3' end?" help="Trim from 3' end until window mean quality is above threshold."/>
-        <param argument="--cut_window_size" type="integer" optional="true" label="Sliding window size" help="Window size shared by cut_front, cut_tail, cut_sliding. Default is 4"/>
-        <param argument="--cut_mean_quality" type="integer" optional="true" label="Mean quality threshold" help="Mean quality required for cutting. Default: 20"/>
-        <param argument="--cut_front_window_size" type="integer" optional="true" 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" 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" 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" label="Tail mean quality" help="Override quality threshold for cut_tail only. Default: cut_mean_quality"/>
-        <param argument="--qualified_quality_phred" type="integer" min="0" optional="true" label="Qualified base Phred score" help="Phred quality score that counts as qualified. Default: 15"/>
-        <param argument="--unqualified_percent_limit" type="integer" min="0" max="100" optional="true" label="Unqualified base percentage limit" help="Percent of bases allowed to be below quality threshold. Default: 40"/>
-        <param argument="--n_base_limit" type="integer" optional="true" label="N base limit" help="Reads with more than this number of N bases are discarded. Default: 5"/>
-        <param argument="--mean_qual" type="integer" optional="true" label="Minimum mean quality" help="Reads with mean quality below this are discarded. Default: 0"/>
-        <param argument="--disable_length_filtering" type="boolean" truevalue="--disable_length_filtering" falsevalue="" checked="false" label="Disable length filtering?" help="Length filtering is enabled by default. Enable this to disable it."/>
-        <param argument="--length_required" type="integer" optional="true" label="Minimum read length" help="Reads shorter than this will be discarded. Default: 15"/>
-        <param argument="--length_limit" type="integer" optional="true" label="Maximum read length" help="Reads longer than this will be discarded. Default: 0 (no limit)"/>
-        <param argument="--low_complexity_filter" type="boolean" truevalue="--low_complexity_filter" falsevalue="" checked="false" label="Enable low complexity filter?" help="Enable low complexity filtering."/>
-        <param argument="--complexity_threshold" type="integer" min="0" max="100" optional="true" label="Complexity threshold (%)" help="Minimum required sequence complexity (0–100). Default: 30"/>
-        <param argument="--failed_out" type="boolean" truevalue="--failed_out" falsevalue="" checked="false" label="Save failed reads?" help="Enable this to write failed reads to a separate FASTQ file."/>
+
+        <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
+            <conditional name="adapter_trim">
+                <param type="select" argument="--disable_adapter_trimming" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled.">
+                    <option value="no" selected="true">NO</option>
+                    <option value="yes">YES</option>
+                </param>
+                <when value="no">
+                    <param argument="--start_adapter" type="text" optional="true" label="Adapter sequence for read start" help="The adapter sequence (uppercase only) at read start (5'). Leave blank to auto-detect.">
+                        <sanitizer invalid_char="" >
+                            <valid initial="none">
+                                <add value="A"/>
+                                <add value="T"/>
+                                <add value="C"/>
+                                <add value="G"/>
+                            </valid>
+                        </sanitizer>
+                    </param>
+                    <param argument="--end_adapter" type="text" optional="true" label="Adapter sequence for read end" help="The adapter sequence (uppercase only) at read end (3'). Leave blank to auto-detect.">
+                        <sanitizer invalid_char="">
+                            <valid initial="none">
+                                <add value="A"/>
+                                <add value="T"/>
+                                <add value="C"/>
+                                <add value="G"/>
+                            </valid>
+                        </sanitizer>
+                    </param>
+                    <param argument="--adapter_fasta" type="data" format="fasta" optional="true" label="FASTA file with adapter sequences" help="Specify a FASTA file to trim the reads by all the sequences in this FASTA file."/>
+                    <param argument="--distance_threshold" type="float" optional="true" value="0.25" min="0.0" max="1.0" label="Adapter Distance Threshold" help="Threshold of sequence-adapter-distance/adapter-length (0.0 ~ 1.0), Higher values increase adapter detection sensitivity. ([0.25])" />
+                    <param argument="--trimming_extension" type="integer" value="10" min="0" max="50" label="Adapter trimming extension" help="When an adapter is detected, extend the trimming to make cleaner trimming, default 10 means trimming 10 bases more [10]."/>
+                </when>
+                <when value="yes"/>
+            </conditional>
+        </section>
+ 
+        <section name="global_trimming_options" title="Global trimming options" expanded="False">
+            <param argument="--trim_front" type="integer" optional="true" label="Trim front (5') of read" help="Trim this many bases from the start (5') of each read. Default: 0."/>
+            <param argument="--trim_tail" type="integer" optional="true" label="Trim tail (3') of read" help="Trim this many bases from the end (3') of each read. Default: 0."/>
+        </section>
+
+        <!-- Filter Options -->
+        <section name="filter_options" title="Filter Options">
+            <section name="quality_filtering_options" title="Quality filtering options" expanded="True">
+                <conditional name="qual_filt"> 
+                    <param argument="--disable_quality_filtering" type="select" label="Disable quality filtering" help="Quality filtering is enabled by default. If this option is specified, quality filtering is disabled.">
+                        <option value="no" selected="true">NO</option>
+                        <option value="yes">YES</option>
+                    </param>
+                    <when value="no">
+                        <param argument="--qualified_quality_phred" type="integer" optional="true" min="0" max="60" value="15" label="Qualified quality phred" help="The quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified."/>
+                        <param argument="--unqualified_percent_limit" type="integer" optional="true" min="0" max="100" value="40" label="Unqualified percent limit" help="How many percent of bases are allowed to be unqualified (0~100). Default 40 means 40%."/>
+                        <param argument="--n_base_limit" type="integer" optional="true" value="5" label="N base limit" help="If a read's number of N base is &gt;n_base_limit, then this read is discarded. Default is 5."/>
+                        <param argument="--mean_qual" type="integer" optional="true" value="0" min="0" max="60" label="Mean read quality" help="If a read's mean_qual quality score &lt;  mean_qual, then this read is discarded. Default 0 means no requirement."/>
+                    </when>
+                    <when value="yes"/>
+                </conditional>
+            </section>
+
+            <section name="length_filtering_options" title="Length filtering options" expanded="True">
+                <conditional name="len_filt">
+                    <param argument="--disable_length_filtering" type="select" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled.">
+                        <option value="no" selected="true">NO</option>
+                        <option value="yes">YES</option>
+                    </param>
+                    <when value="no">
+                        <param argument="--length_required" type="integer" optional="true" value="15" min="1" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/>
+                        <param argument="--length_limit" type="integer" optional="true" value="0" min="0" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/>
+                    </when>
+                    <when value="yes"/>
+                </conditional>
+            </section>
+
+            <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
+                <conditional name="compl_filt">
+                    <param argument="--low_complexity_filter" type="select" label="Enable low complexity filter" help="The complexity is defined as the percentage of bases that is different from its next base. Default is No">
+                        <option value="no" selected="true">NO</option>
+                        <option value="yes">YES</option>
+                    </param>
+                    <when value="yes">
+                        <param argument="--complexity_threshold" type="integer" optional="true" min="0" max="100" value="30" label="Complexity threshold (%)" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>
+                    </when>
+                    <when value="no"/>
+                </conditional>
+            </section>
+        </section>
+
+        <!-- Read Modification Options -->
+        <section name="read_mod_options" title="Read Modification Options">
+            <section name="polyx_tail_trimming" title="Polyx trimming on tail" expanded="False">
+                <conditional name="polyx">
+                    <param argument="--trim_poly_x" type="select" label="PolyX tail trimming" help="Enable polyX trimming on 3' ends.">
+                        <option value="no" selected="true">NO</option>
+                        <option value="yes">YES</option>
+                    </param>
+                    <when value="yes">
+                        <param argument="--poly_x_min_len" type="integer" optional="true" value="10" label="PolyX minimum length"
+                        help="The minimum length to detect polyX in the read tail. 10 by default."/>
+                    </when>
+                    <when value="no"/>
+                </conditional>
+            </section>
+
+            <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
+                <conditional name="qual_trim">
+                    <param name="trim_side" type="select" label="Activate trimming by quality" help="Enable per read trimming by quality on both sides/ front (5') only or tail (3') only, move a sliding window from over the read strating from the specified side, drop the bases in the window if its mean quality &lt; threshold until window mean quality is above threshold">
+                        <option value="none" selected="true">No quality trimming</option>
+                        <option value="both">quality trimming from both sides</option>
+                        <option value="front">quality trimming from front (5') only</option>
+                        <option value="tail">quality trimming from tail (3') only</option>
+                    </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"/>
+                    </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"/>
+                    </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"/>
+                    </when>
+                </conditional>
+            </section>
+        </section>
+
+        <section name="output_options" title="Output Options" expanded="False">
+            <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="Fastplong provides a QC report for the data before and after filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
+            <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
+            <param argument="--failed_out" type="boolean" truevalue="--failed_out" falsevalue="" checked="false" label="Save failed reads?" help="Enable this to write failed reads to a separate FASTQ file."/>
+        </section>
     </inputs>
+
     <outputs>
-        <data name="output" format="fastq" label="Filtered Output FASTQ"/>
-        <data name="failed_out_reads" format="fastq" from_work_dir="failed_reads.fastq" label="Failed Reads FASTQ">
-            <filter>failed_out</filter>
+        <data name="out" format_source="in" label="${tool.name} on ${on_string}: Reads FASTQ output"/>
+        <data name="report_html" format="html" from_work_dir="fastplong.html" label="${tool.name} on ${on_string}: HTML report">
+            <filter>output_options['report_html'] is True</filter>
+        </data>
+        <data name="report_json" format="json" from_work_dir="fastplong.json" label="${tool.name} on ${on_string}: JSON report">
+            <filter>output_options['report_json'] is True</filter>
+        </data>
+        <data name="failed_out" format="fastq" from_work_dir="failed_reads.fastq" label="${tool.name} on ${on_string}: Failed Reads FASTQ">
+            <filter>output_options['failed_out'] is True</filter>
         </data>
-        <data name="json_output_default" format="json" from_work_dir="fastplong.json" label="JSON Report (default)"/>
-        <data name="html_output_default" format="html" from_work_dir="fastplong.html" label="HTML Report (default)"/>
     </outputs>
+
     <tests>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="2">
             <param name="in" value="input.fastq"/>
-            <output name="output" file="output.fastq"/>
+            <output name="report_html">
+                <assert_contents>
+                    <has_text text="html"/>
+                    <has_text text="fastplong report"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="3">
             <param name="in" value="input.fastq"/>
-            <param name="reads_to_process" value="3"/>
-            <output name="output" file="output_reads_to_process.fastq"/>
+            <section name="output_options">
+                <param name="report_json" value="true"/>
+            </section>
+            <output name="out" file="output.fastq"/>
+            <output name="report_json">
+				<assert_contents>
+					<has_text text='summary": {'/>
+					<has_text text='fastplong_version": "@TOOL_VERSION@'/>
+				</assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="2">
+            <param name="in" value="input.fastq"/>
+            <output name="out" file="output.fastq"/>
+        </test>
+        <test expect_num_outputs="2">
             <param name="in" value="input.fastq"/>
-            <param name="failed_out" value="true"/>
-            <output name="failed_out_reads" value="output_failed_out.fastq"/>
+            <param name="reads_to_process" value="3"/>
+            <output name="out" file="output_reads_to_process.fastq"/>
+        </test>
+        <test expect_num_outputs="3">
+            <param name="in" value="input.fastq"/>
+            <section name="output_options">
+                <param name="failed_out" value="true"/>
+            </section>
+            <output name="failed_out" value="output_failed_out.fastq"/>
         </test>
     </tests>
-    <help>
-    **Fastplong: Filter and trim long reads**
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+fastplong_ is a tool designed to provide fast all-in-one preprocessing for long reads FASTQ files. This tool is developed in C++ with multithreading supported to
+afford high performance.
+
+*Features*
+
+1. Filter out bad reads (too low quality, too short, or too many N...)
 
-        This tool wraps the `fastplong` command-line tool to allow filtering and trimming of long reads in FASTQ format.
+2. Cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster)
+
+3. Trim all reads in front and tail
+
+4. Cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
+
+5. Trim polyX in 3' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)
+
+6. Report JSON format result for further interpreting
+
+7. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
+
 
-    **Inputs**
-    - A FASTQ file containing reads and optional parameters to control trimming, quality filtering, adapter detection, and more.
+-----
+
+**Inputs**
+
+Single-end FASTQ or FASTQ.GZ long reads
+
+-----
+
+**Outputs**
+
+    * Processed reads
 
-    **Outputs**
-    - A filtered FASTQ file with trimmed reads, HTML and JSON report and an optional FASTQ file of failed reads.
+Optionally, under **Output Options** you can choose to output
+
+    * HTML report (default is Yes)
+    * JSON report (compatible with MultiQC)
+    * Failed reads (default is No)
 
-    For more information, see https://github.com/OpenGene/fastplong
-    </help>
+**More Information**
+
+- **Official Repository**: [GitHub - OpenGene/fastplong](https://github.com/OpenGene/fastplong)
+
+.. _fastplong: https://github.com/OpenGene/fastplong
+
+]]></help>
     <citations>
         <citation type="doi">10.1002/imt2.107</citation>
         <citation type="doi">10.1093/bioinformatics/bty560</citation>