From 346ee8547ccbdc6f692c2314f4e7956caaec4fe2 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Thu, 22 Aug 2024 15:40:11 +0000
Subject: [PATCH 1/3] Updating tools/nextdenovo from version 2.5.0 to 2.5.2

---
 tools/nextdenovo/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/nextdenovo/macros.xml b/tools/nextdenovo/macros.xml
index 778ea5ac06..608441a66c 100644
--- a/tools/nextdenovo/macros.xml
+++ b/tools/nextdenovo/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.5.0</token>
+    <token name="@TOOL_VERSION@">2.5.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>

From 2aee5f1025eeb9c43b5c51585258b802f5903d09 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Thu, 22 Aug 2024 21:11:02 +0200
Subject: [PATCH 2/3] update, test still fails

---
 tools/nextdenovo/nextdenovo.xml | 43 +++++++++++++++------------------
 1 file changed, 19 insertions(+), 24 deletions(-)

diff --git a/tools/nextdenovo/nextdenovo.xml b/tools/nextdenovo/nextdenovo.xml
index cdcf937489..78baa16a8a 100644
--- a/tools/nextdenovo/nextdenovo.xml
+++ b/tools/nextdenovo/nextdenovo.xml
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="biotools"/>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <version_command>nextDenovo --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p './read_files' &&
@@ -49,7 +49,7 @@
         ]]></configfile>
     </configfiles>
     <inputs>
-        <param name="input_reads" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" multiple="true" label="Sequence reads"/>
+        <param name="input_reads" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Sequence reads" multiple="true"/>
         <param name="task" type="select" label="Task">
             <option value="all">All</option>
             <option value="correct">Correct: only do the correction step</option>
@@ -71,8 +71,7 @@
                 <option value="seed">Seed cutoff</option>
             </param>
             <when value="genome">
-                <param name="genome_size" type="text" value="" optional="true" label="Estimated genome size" help="Estimated genome size, suffix K/M/G recognized, used to 
-                calculate seed_cutoff/seed_cutfiles/blocksize and average depth, it can be omitted when manually setting seed_cutoff. Spaces are not allowed.">
+                <param name="genome_size" type="text" value="" optional="true" label="Estimated genome size" help="Estimated genome size, suffix K/M/G recognized, used to                  calculate seed_cutoff/seed_cutfiles/blocksize and average depth, it can be omitted when manually setting seed_cutoff. Spaces are not allowed.">
                     <sanitizer invalid_char="">
                         <valid initial="string.letters,string.digits">
                             <add value="."/>
@@ -80,51 +79,47 @@
                     </sanitizer>
                     <validator type="regex">[0-9KMGkmg.]+</validator>
                 </param>
-                <param name="seed_depth" type="integer" min="0" value="45" label="Seed depth" help="Expected seed depth, used to calculate seed_cutoff, co-use with 
-                    genome_size, you can try to set it 30-45 to get a better assembly result." />
+                <param name="seed_depth" type="integer" min="0" value="45" label="Seed depth" help="Expected seed depth, used to calculate seed_cutoff, co-use with                      genome_size, you can try to set it 30-45 to get a better assembly result."/>
             </when>
             <when value="seed">
-                <param name="seed_cutoff" type="integer" min="0" value="0" optional="true" label="Seed cutoff" help="Minimum seed length. Set it to 0 for calculating it automatically." />
+                <param name="seed_cutoff" type="integer" min="0" value="0" optional="true" label="Seed cutoff" help="Minimum seed length. Set it to 0 for calculating it automatically."/>
             </when>
         </conditional>
-        <param name="blocksize" type="text" value="10g" label="Block size" help="Block size for parallel running, split non-seed reads into small files, the maximum size of 
-            each file is blocksize.">
+        <param name="blocksize" type="text" value="10g" label="Block size" help="Block size for parallel running, split non-seed reads into small files, the maximum size of              each file is blocksize.">
             <sanitizer invalid_char="">
                 <valid initial="string.letters,string.digits"/>
             </sanitizer>
             <validator type="regex">[0-9KMGkmg]+</validator>
         </param>
         <section name="ovl_parameters" title="OVL sort parameters" expanded="true">
-            <param name="max_depth_overlap" type="integer" min="0" value="40" label="Max depth of each overlap" help="This value should be equal or smaller than 
-                the average sequencing depth." />
+            <param name="max_depth_overlap" type="integer" min="0" value="40" label="Max depth of each overlap" help="This value should be equal or smaller than                  the average sequencing depth."/>
             <param name="max_over_hang_length" type="integer" min="0" value="300" label="Max over hang length to filter"/>
         </section>
         <section name="minimap_parameters" title="Minimap2 parameters" expanded="true">
             <param name="minlen" type="integer" min="0" value="500" label="Minimum overlap length"/>
             <param name="minmatch" type="integer" min="0" value="100" label="Minimum match length"/>
-            <param name="minide" type="float" min="0" value="0.05" max="1" label="Minimum identity"/>
-            <param name="kn" type="integer" min="0" value="17" max="28" label="K-mer size"/>
+            <param name="minide" type="float" min="0" max="1" value="0.05" label="Minimum identity"/>
+            <param name="kn" type="integer" min="0" max="28" value="17" label="K-mer size"/>
             <param name="wn" type="integer" min="0" value="10" label="Minimizer window size"/>
             <param name="cn" type="integer" min="0" value="20" label="Re-align for every n reads"/>
             <param name="maxhan1" type="integer" min="0" value="5000" label="Maximum over hang length for re-align"/>
             <param name="maxhan2" type="integer" min="0" value="500" label="Maximum over hang length for filtering contained reads"/>
         </section>
         <section name="correction_options" title="Correction options" expanded="true">
-            <param name="split" type="boolean" truevalue="--split" falsevalue="" checked="false" label="Split" help="Split the corrected seed with un-corrected regions" />
-            <param name="fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Fast" help="0.5-1 times faster mode with a little lower accuracy." />
+            <param name="split" type="boolean" truevalue="--split" falsevalue="" checked="false" label="Split" help="Split the corrected seed with un-corrected regions"/>
+            <param name="fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Fast" help="0.5-1 times faster mode with a little lower accuracy."/>
         </section>
         <section name="np" title="NextGraph parameters">
             <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Disable pre-filter chimeric reads."/>
             <param argument="-G" type="boolean" truevalue="-G" falsevalue="" checked="false" label="Retain potential chimeric edges."/>
             <param argument="-k" type="boolean" truevalue="-k" falsevalue="" checked="false" label="Delete complex bubble paths."/>
-            <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Output alternative contigs" 
-                help="For highly heterozygous genomes, it will increase assembly size."/>
+            <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Output alternative contigs" help="For highly heterozygous genomes, it will increase assembly size."/>
             <param argument="-a" type="select" label="Output format">
                 <option value="1">FASTA</option>
                 <option value="3">GFA</option>
             </param>
             <param argument="-E" type="integer" min="0" value="1000" label="Minimum contig length"/>
-            <param argument="-q" type="integer" min="0" value="0" label="Minimum short branch length" help="By default it is disabled (value = 0)." />
+            <param argument="-q" type="integer" min="0" value="0" label="Minimum short branch length" help="By default it is disabled (value = 0)."/>
             <param argument="-i" type="float" min="0" max="1" value="0.1" label="Minimum identity of alignmnents"/>
             <param argument="-I" type="float" min="0" max="1" value="0.7" label="Minimum test-to-best identity ratio"/>
             <param argument="-R" type="float" min="0" max="1" value="0" label="Maximum test-to-best identity ratio"/>
@@ -152,10 +147,10 @@
         <data name="stats" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: stats">
             <filter>task != 'correct'</filter>
         </data>
-        <data name="asmp" format="txt" from_work_dir="03.ctg_graph/nd.asm.p.fasta" label="${tool.name} on ${on_string}: nd.asm.p.fasta">
+        <data name="asmp" format="fasta" from_work_dir="03.ctg_graph/nd.asm.p.fasta" label="${tool.name} on ${on_string}: nd.asm.p.fasta">
             <filter>task != 'correct'</filter>
         </data>
-        <data name="asm" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: nd.asm.p.fasta">
+        <data name="asm_fasta_stat" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: nd.asm.fasta.stat">
             <filter>task != 'correct'</filter>
         </data>
         <data name="asm" format="txt" from_work_dir="02.cns_align/01.seed_cns.sh.work/seed_cns3" label="${tool.name} on ${on_string}: corrected">
@@ -193,7 +188,7 @@
                 <param name="seed_depth" value="45"/>
             </conditional>
             <assert_stderr>
-                <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully." />
+                <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully."/>
             </assert_stderr>
         </test>
         <test expect_failure="true">
@@ -207,7 +202,7 @@
                 <param name="seed_depth" value="45"/>
             </conditional>
             <assert_stderr>
-                <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully." />
+                <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully."/>
             </assert_stderr>
         </test>
     </tests>
@@ -216,5 +211,5 @@
         a "correct-then-assemble" strategy similar to canu (no correction step for PacBio HiFi reads), but 
         requires significantly less computing resources and storages.
     ]]></help>
-    <expand macro="citations" />
-</tool>
\ No newline at end of file
+    <expand macro="citations"/>
+</tool>

From d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 7 Oct 2024 14:25:06 +0200
Subject: [PATCH 3/3] style updates

---
 tools/nextdenovo/macros.xml     | 10 +---------
 tools/nextdenovo/nextdenovo.xml |  8 ++++----
 2 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/tools/nextdenovo/macros.xml b/tools/nextdenovo/macros.xml
index 608441a66c..863ce3695f 100644
--- a/tools/nextdenovo/macros.xml
+++ b/tools/nextdenovo/macros.xml
@@ -13,15 +13,7 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-                @misc{githubNextDenovo,
-                author = {Jiang, Hu},
-                year = {2022},
-                title = {NextDenovo},
-                publisher = {GitHub},
-                journal = {GitHub repository},
-                url = {https://github.com/Nextomics/NextDenovo}}
-            </citation>
+            <citation type="doi">10.1186/s13059-024-03252-4</citation>
         </citations>
     </xml>
 </macros>
diff --git a/tools/nextdenovo/nextdenovo.xml b/tools/nextdenovo/nextdenovo.xml
index 78baa16a8a..0a23b78ea5 100644
--- a/tools/nextdenovo/nextdenovo.xml
+++ b/tools/nextdenovo/nextdenovo.xml
@@ -71,7 +71,7 @@
                 <option value="seed">Seed cutoff</option>
             </param>
             <when value="genome">
-                <param name="genome_size" type="text" value="" optional="true" label="Estimated genome size" help="Estimated genome size, suffix K/M/G recognized, used to                  calculate seed_cutoff/seed_cutfiles/blocksize and average depth, it can be omitted when manually setting seed_cutoff. Spaces are not allowed.">
+                <param name="genome_size" type="text" value="" optional="true" label="Estimated genome size" help="Estimated genome size, suffix K/M/G recognized, used to calculate seed_cutoff/seed_cutfiles/blocksize and average depth, it can be omitted when manually setting seed_cutoff. Spaces are not allowed.">
                     <sanitizer invalid_char="">
                         <valid initial="string.letters,string.digits">
                             <add value="."/>
@@ -79,20 +79,20 @@
                     </sanitizer>
                     <validator type="regex">[0-9KMGkmg.]+</validator>
                 </param>
-                <param name="seed_depth" type="integer" min="0" value="45" label="Seed depth" help="Expected seed depth, used to calculate seed_cutoff, co-use with                      genome_size, you can try to set it 30-45 to get a better assembly result."/>
+                <param name="seed_depth" type="integer" min="0" value="45" label="Seed depth" help="Expected seed depth, used to calculate seed_cutoff, co-use with genome_size, you can try to set it 30-45 to get a better assembly result."/>
             </when>
             <when value="seed">
                 <param name="seed_cutoff" type="integer" min="0" value="0" optional="true" label="Seed cutoff" help="Minimum seed length. Set it to 0 for calculating it automatically."/>
             </when>
         </conditional>
-        <param name="blocksize" type="text" value="10g" label="Block size" help="Block size for parallel running, split non-seed reads into small files, the maximum size of              each file is blocksize.">
+        <param name="blocksize" type="text" value="10g" label="Block size" help="Block size for parallel running, split non-seed reads into small files, the maximum size of each file is blocksize.">
             <sanitizer invalid_char="">
                 <valid initial="string.letters,string.digits"/>
             </sanitizer>
             <validator type="regex">[0-9KMGkmg]+</validator>
         </param>
         <section name="ovl_parameters" title="OVL sort parameters" expanded="true">
-            <param name="max_depth_overlap" type="integer" min="0" value="40" label="Max depth of each overlap" help="This value should be equal or smaller than                  the average sequencing depth."/>
+            <param name="max_depth_overlap" type="integer" min="0" value="40" label="Max depth of each overlap" help="This value should be equal or smaller than the average sequencing depth."/>
             <param name="max_over_hang_length" type="integer" min="0" value="300" label="Max over hang length to filter"/>
         </section>
         <section name="minimap_parameters" title="Minimap2 parameters" expanded="true">