New tool addition: KneadData #7498

xens25 · 2025-12-01T12:17:09Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

SaimMomin12 · 2025-12-01T12:33:33Z

tools/kneaddata/.shed.yml

+categories:
+  - Sequence Analysis
+  - Metagenomics
+  - Quality Control


Suggested change

- Quality Control

SaimMomin12 · 2025-12-01T12:34:32Z

tools/kneaddata/kneaddata.xml

@@ -0,0 +1,272 @@
+<tool id="kneaddata" name="KneadData" version="0.12.1+galaxy0" python_template_version="3.5" profile="21.05">


Suggested change

<tool id="kneaddata" name="KneadData" version="0.12.1+galaxy0" python_template_version="3.5" profile="21.05">

<tool id="kneaddata" name="KneadData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

Please introduce the above tokens in the macros.xml file

SaimMomin12 · 2025-12-01T12:35:09Z

tools/kneaddata/kneaddata.xml

+    <requirements>
+        <requirement type="package" version="0.12.3">kneaddata</requirement>
+        <requirement type="package" version="0.40">trimmomatic</requirement>
+        <requirement type="package" version="2.5.4">bowtie2</requirement>
+        <requirement type="package" version="4.09.1">trf</requirement>
+        <requirement type="package" version="0.12.1">fastqc</requirement>
+    </requirements>


This can go in macros.xml. Wondering if these dependencies are already part of Kneaddata or does one explicitly need them?

SaimMomin12 · 2025-12-01T12:35:27Z

tools/kneaddata/kneaddata.xml

+                <option value="s">Single read</option> 
+                <option value="p">Paired reads</option> 


Suggested change

<option value="s">Single read</option>

<option value="p">Paired reads</option>

<option value="single">Single read</option>

<option value="paired">Paired reads</option>

SaimMomin12 · 2025-12-01T12:36:08Z

tools/kneaddata/kneaddata.xml

+            </param> 
+
+            <when value="s"> 
+                <param name="single_read" type="data" format="fastq" label="Single Read"/> 


Suggested change

<param name="single_read" type="data" format="fastq" label="Single Read"/>

<param name="single_read" type="data" format="fastqsanger" label="Single Read"/>

Does it also support fastq.gz?

SaimMomin12 · 2025-12-01T12:36:17Z

tools/kneaddata/kneaddata.xml

+            <when value="s"> 
+                <param name="single_read" type="data" format="fastq" label="Single Read"/> 
+            </when> 
+            <when value="p"> 


Suggested change

<when value="p">

<when value="paired">

SaimMomin12 · 2025-12-01T12:36:39Z

tools/kneaddata/kneaddata.xml

+        <param name="number_threads" type="integer" value="1" label="Number of threads"/>
+
+        <param name="number_processes" type="integer" value="1" label="Number of processes"/>


Suggested change

<param name="number_threads" type="integer" value="1" label="Number of threads"/>

<param name="number_processes" type="integer" value="1" label="Number of processes"/>

This is not required

SaimMomin12 · 2025-12-01T12:36:54Z

tools/kneaddata/kneaddata.xml

+
+        <section name="trimmomatic" title="Trimmomatic arguments" >
+
+            <param name="max_memory" type="text" value="500m" label="Maximum memory for Trimmomatic"/>


Suggested change

<param name="max_memory" type="text" value="500m" label="Maximum memory for Trimmomatic"/>

SaimMomin12 · 2025-12-01T12:39:37Z

tools/kneaddata/kneaddata.xml

+
+            <conditional name="trimmomatic_options">
+                <param name="select_option" type="select" label="Trimmomatic settings"> 
+                    <option value="d">Default settings</option> 


Better names for option values?

SaimMomin12 · 2025-12-01T12:40:41Z

tools/kneaddata/.shed.yml

+  quality filtering, and removal of host contamination using
+  Bowtie2/TRIMMOMATIC/TRF.
+homepage_url: https://github.com/biobakery/kneaddata
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata


Suggested change

remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata

remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata

SaimMomin12 · 2025-12-01T12:40:49Z

tools/kneaddata/.shed.yml

+owner: iuc
+type: unrestricted
+description: Quality control and contaminant removal for metagenomic data
+long_description: >


Suggested change

long_description: >

long_description: |

SaimMomin12 · 2025-12-01T12:41:02Z

tools/kneaddata/.shed.yml

+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata
+categories:
+  - Metagenomics
+  - Statistics


Suggested change

- Statistics

- Sequence Analysis

SaimMomin12 · 2025-12-01T13:27:59Z

tools/kneaddata/kneaddata.xml

+        <requirement type="package" version="0.12.1">fastqc</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        kneaddata 


Suggested change

kneaddata

mkdir -p results/

kneaddata

SaimMomin12 · 2025-12-01T13:28:09Z

tools/kneaddata/kneaddata.xml

+            -i1 "$read_type.forward_read" 
+            -i2 "$read_type.backward_read" 
+        #end if
+        -o "output_dir"


Suggested change

-o "output_dir"

-o results/

SaimMomin12 · 2025-12-01T16:03:56Z

tools/kneaddata/.shed.yml

+  metagenomic and metatranscriptomic sequencing data, especially
+  data from microbiome experiments. It performs adapter trimming,
+  quality filtering, and removal of host contamination using
+  Bowtie2/TRIMMOMATIC/TRF.


Suggested change

Bowtie2/TRIMMOMATIC/TRF.

Bowtie2, TRIMMOMATIC and TRF.

SaimMomin12 · 2025-12-01T16:04:50Z

tools/kneaddata/kneaddata.xml

+        #if "$output_prefix"
+            --output-prefix "$output_prefix"
+        #end if


I would be in favor of removing this parameter

SaimMomin12 · 2025-12-01T16:05:00Z

tools/kneaddata/kneaddata.xml

+        --threads "$number_threads"
+        --processes "$number_processes"


Suggested change

--threads "$number_threads"

--processes "$number_processes"

SaimMomin12 · 2025-12-01T16:08:50Z

tools/kneaddata/kneaddata.xml

+            <param name="number_threads" value="1"/>
+            <param name="number_processes" value="1"/>


Suggested change

<param name="number_threads" value="1"/>

<param name="number_processes" value="1"/>

SaimMomin12 · 2025-12-01T16:09:49Z

tools/kneaddata/kneaddata.xml

+            </section>
+            <section name="read_type">
+                <param name="select_read_type" value="s"/>
+                <param name="single_read" value="28C.single.fastq"/>


Suggested change

<param name="single_read" value="28C.single.fastq"/>

<param name="single_read" value="test_single.fastq"/>

SaimMomin12 · 2025-12-01T16:10:07Z

tools/kneaddata/kneaddata.xml

+                <param name="forward_read" value="28C.R1.fastq"/>
+                <param name="backward_read" value="28C.R2.fastq"/>
+            </section>
+            <output name="paired_forward" file="paired_forward.fastq"/>


Suggested change

<output name="paired_forward" file="paired_forward.fastq"/>

<output name="paired_forward" file="test_paired_1.fastq"/>

SaimMomin12 · 2025-12-01T16:10:19Z

tools/kneaddata/kneaddata.xml

+                <param name="backward_read" value="28C.R2.fastq"/>
+            </section>
+            <output name="paired_forward" file="paired_forward.fastq"/>
+            <output name="paired_backward" file="paired_backward.fastq"/>


Suggested change

<output name="paired_backward" file="paired_backward.fastq"/>

<output name="paired_backward" file="test_paired_2.fastq"/>

SaimMomin12 · 2025-12-01T16:11:14Z

tools/kneaddata/kneaddata.xml

+    usage: kneaddata [-h] [--version] [-v] [-i1 INPUT1] [-i2 INPUT2]
+                 [-un UNPAIRED]  -o OUTPUT_DIR
+                 [-db REFERENCE_DB] [--bypass-trim] [--run-trim-repetitive]
+                 [--output-prefix OUTPUT_PREFIX] [-t &lt;1&gt;] [-p &lt;1&gt;]
+                 [-q {phred33,phred64}] [--run-bmtagger]
+                 [--run-fastqc-start] [--run-fastqc-end] [--store-temp-output]
+                 [--cat-final-output]
+                 [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--log LOG]
+                 [--trimmomatic TRIMMOMATIC_PATH] [--max-memory MAX_MEMORY]
+                 [--trimmomatic-options TRIMMOMATIC_OPTIONS]
+                 [--bowtie2 BOWTIE2_PATH] [--bowtie2-options BOWTIE2_OPTIONS]
+                 [--bmtagger BMTAGGER_PATH] [--trf TRF_PATH] [--match MATCH]
+                 [--mismatch MISMATCH] [--delta DELTA] [--pm PM] [--pi PI]
+                 [--minscore MINSCORE] [--maxperiod MAXPERIOD]
+                 [--fastqc FASTQC_PATH]
+
+    KneadData
+
+    options:
+
+
+    -h, --help  show this help message and exit
+    -v, --verbose  additional output is printed
+    --version  show program's version number and exit
+    -i INPUT, --input INPUT  input FASTQ file (add a second argument instance to run with paired input files)
+    -o OUTPUT_DIR, --output OUTPUT_DIR  directory to write output files
+    --db REFERENCE_DB, --reference-db REFERENCE_DB  location of reference database
+    --run-trim-repetitive  Option to trim repetitive/overrepresented sequences generated by FASTQC reports 
+    --bypass-trim  bypass the trim step
+    --output-prefix OUTPUT_PREFIX  prefix for all output files  [ DEFAULT : $SAMPLE_kneaddata ]
+    -t <1>, --threads <1>  number of threads  [ Default : 1 ]
+    -p <1>, --processes <1>  number of processes  [ Default : 1 ]
+    -q <quality>, --quality-scores <quality>  quality scores [phred33|phred64] [DEFAULT: phred33]
+    --run-bmtagger  run BMTagger instead of Bowtie2 to identify contaminant reads
+    --bypass-trf  option to bypass the removal of tandem repeats
+    --run-fastqc-start  run fastqc at the beginning of the workflow
+    --run-fastqc-end  run fastqc at the end of the workflow
+    --store-temp-output  store temp output files [ DEFAULT : temp output files are removed ]
+    --cat-final-output  concatenate all final output files [ DEFAULT : final output is not concatenated ]
+    --log-level <DEBUG|INFO|WARNING|ERROR|CRITICAL>  level of log messages [DEFAULT: DEBUG]
+    --log LOG  log file [ DEFAULT : $OUTPUT_DIR/$SAMPLE_kneaddata.log ]
+    --trimmomatic TRIMMOMATIC_PATH  path to trimmomatic [ DEFAULT : $PATH ]
+    --max-memory MAX_MEMORY  max amount of memory [ DEFAULT : 500m ]
+    --trimmomatic-options TRIMMOMATIC_OPTIONS  options for trimmomatic [ DEFAULT : SLIDINGWINDOW:4:20 MINLEN:50 ]
+      MINLEN is set to 50 percent of total input read length. The user can alternatively specify a length (in bases) for MINLEN.
+    --sequencer-source  options for sequencer-source [ DEFAULT: NexteraPE]  Available sequencers: ["NexteraPE","TruSeq2","TruSeq3"]
+    --bowtie2 BOWTIE2_PATH  path to bowtie2 [ DEFAULT : $PATH ]
+    --bowtie2-options BOWTIE2_OPTIONS  options for bowtie2 [ DEFAULT : --very-sensitive ]
+    --bmtagger BMTAGGER_PATH  path to BMTagger  [ DEFAULT : $PATH ]
+    --bypass-trf  bypass the TRF step
+    --trf TRF_PATH  path to TRF [ DEFAULT : $PATH ]
+    --mismatch MISMATCH  mismatching penalty  [ DEFAULT : 7 ]
+    --delta DELTA  indel penalty  [ DEFAULT : 7 ]
+    --pm PM  match probability  [ DEFAULT : 80 ]
+    --pi PI  indel probability  [ DEFAULT : 10 ]
+    --minscore MINSCORE  minimum alignment score to report  [ DEFAULT : 50 ]
+    --maxperiod MAXPERIOD  maximum period size to report  [ DEFAULT : 500 ]
+    --fastqc FASTQC_PATH  path to fastqc [ DEFAULT : $PATH ]
+


A better help could be what is KneadData tool, what does it do, what inputs it requires, what outputs it gives out etc. Perhaps explanation of a few important parameters

fixed help section added bmtagger added all missing arguments added additional outputs

Updated long description formatting and corrected repository URL.

- Updated tool XML with all arguments - Updated macros.xml

SaimMomin12 · 2025-12-08T12:36:08Z

tools/kneaddata/kneaddata.xml

+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p results/ ;


Suggested change

mkdir -p results/ ;

mkdir -p results/

SaimMomin12 · 2025-12-08T12:36:17Z

tools/kneaddata/kneaddata.xml

+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p results/ ;
+


Suggested change

SaimMomin12 · 2025-12-08T12:37:11Z

tools/kneaddata/kneaddata.xml

+        $cat_final_output
+
+    ]]></command>
+


Suggested change

SaimMomin12 · 2025-12-08T12:37:57Z

tools/kneaddata/kneaddata.xml

+    <inputs>
+
+        <conditional name="read_type"> 
+            <param name="select_read_type" type="select" label="Read type" help="Specify whether your sequencing data is single-end (one file) or paired-end (two files)."> 


Suggested change

<param name="select_read_type" type="select" label="Read type" help="Specify whether your sequencing data is single-end (one file) or paired-end (two files).">

<param name="select_read_type" type="select" label="Read type" help="Specify your sequencing data type.">

SaimMomin12 · 2025-12-08T12:39:29Z

tools/kneaddata/kneaddata.xml

+            </param> 
+
+            <when value="single"> 
+                <param name="single_read" type="data" format="fastqsanger" label="Single Read"/>  


Can the tool also accomodate fastqsanger.gz

SaimMomin12 · 2025-12-08T13:50:13Z

tools/kneaddata/kneaddata.xml

+            <when value="single"> 
+                <param name="single_read" type="data" format="fastqsanger" label="Single Read"/>  
+            </when> 
+            <when value="paired"> 


You can implement paired_collection input instead of paired input

SaimMomin12 · 2025-12-08T13:52:06Z

tools/kneaddata/kneaddata.xml

+                    <conditional name="reference_genome">
+                        <param name="source" type="select" label="Select reference database source" help="Select a built-in genome index or upload your own FASTA file">
+                            <option value="indexed">Use built-in genome index</option>
+                            <option value="history">Upload custom FASTA file</option>


This is not implemented in the CMD section. If you like, you can also remove it

SaimMomin12 · 2025-12-08T13:52:17Z

tools/kneaddata/kneaddata.xml

+                    <conditional name="reference_genome">
+                        <param name="source" type="select" label="Select reference database source" help="Select a built-in genome index or upload your own FASTA file">
+                            <option value="indexed">Use built-in genome index</option>
+                            <option value="history">Upload custom FASTA file</option>


SaimMomin12 · 2025-12-08T13:52:47Z

tools/kneaddata/kneaddata.xml

+                            <param name="bmtagger_db" type="select" label="Select reference genome database"
+                                help="Select the organism genome to filter out. This genome's reads will be removed as host contamination.">
+                                <options from_data_table="bmtagger_indexes">
+                                    <filter type="sort_by" column="3" />


Please check with the bmtagger data tables from the bmtagger tool

SaimMomin12 · 2025-12-08T13:54:32Z

tools/kneaddata/kneaddata.xml

+        <param name="store_temp" type="boolean" truevalue="--store-temp-output" falsevalue="" label="Keep temporary files" 
+            help="Save temporary/intermediate files generated during processing. This includes alignment files and trimmed intermediate reads. This will 
+            increase the output file size."/>


This can be skipped

xens25 added 3 commits December 1, 2025 12:58

Add KneadData tool wrapper

972c7fd

Add .shed.yml file for kneaddata tool

9d626bc

Fix linting issues: unique output labels, complete shed metadata

93dd153

SaimMomin12 reviewed Dec 1, 2025

View reviewed changes

Fix duplicate output labels for linting

d765919

SaimMomin12 reviewed Dec 1, 2025

View reviewed changes

SaimMomin12 changed the title ~~Add KneadData tool wrapper~~ New tool addition: KneadData Dec 1, 2025

SaimMomin12 mentioned this pull request Dec 1, 2025

New tool request: Host decontamination tools #7438

Open

4 tasks

Add Bowtie2 data tables

ec2560d

SaimMomin12 reviewed Dec 1, 2025

View reviewed changes

xens25 added 6 commits December 8, 2025 13:26

Update kneaddata.xml

7d70bd7

fixed help section added bmtagger added all missing arguments added additional outputs

Add macros.xml

adc65c1

Update .shed.yml

1daf4cc

Updated long description formatting and corrected repository URL.

Add KneadData tool with complete files

1cd225f

- Updated tool XML with all arguments - Updated macros.xml

Add missing test output file kneaddata.log

9b1a59e

Replace large test

7383189

SaimMomin12 reviewed Dec 8, 2025

View reviewed changes

		@@ -0,0 +1,272 @@
		<tool id="kneaddata" name="KneadData" version="0.12.1+galaxy0" python_template_version="3.5" profile="21.05">

		<option value="s">Single read</option>
		<option value="p">Paired reads</option>

	<param name="single_read" type="data" format="fastq" label="Single Read"/>
	<param name="single_read" type="data" format="fastqsanger" label="Single Read"/>

		<param name="number_threads" type="integer" value="1" label="Number of threads"/>

		<param name="number_processes" type="integer" value="1" label="Number of processes"/>


		<section name="trimmomatic" title="Trimmomatic arguments" >

		<param name="max_memory" type="text" value="500m" label="Maximum memory for Trimmomatic"/>

	remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata
	remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata

		<param name="number_threads" value="1"/>
		<param name="number_processes" value="1"/>

	<param name="single_read" value="28C.single.fastq"/>
	<param name="single_read" value="test_single.fastq"/>

	<output name="paired_forward" file="paired_forward.fastq"/>
	<output name="paired_forward" file="test_paired_1.fastq"/>

	<output name="paired_backward" file="paired_backward.fastq"/>
	<output name="paired_backward" file="test_paired_2.fastq"/>

	<param name="select_read_type" type="select" label="Read type" help="Specify whether your sequencing data is single-end (one file) or paired-end (two files).">
	<param name="select_read_type" type="select" label="Read type" help="Specify your sequencing data type.">

New tool addition: KneadData #7498

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New tool addition: KneadData #7498

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xens25 commented Dec 1, 2025

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