New tool addition: KneadData #7498
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| name: kneaddata | ||||||
| owner: iuc | ||||||
| type: unrestricted | ||||||
| description: Quality control and contaminant removal for metagenomic data | ||||||
| long_description: > | ||||||
| KneadData is a tool designed to perform quality control on | ||||||
| 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. | ||||||
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| Bowtie2/TRIMMOMATIC/TRF. | |
| Bowtie2, TRIMMOMATIC and TRF. |
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| 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 |
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| - Statistics | |
| - Sequence Analysis |
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| <tool id="kneaddata" name="KneadData" version="0.12.1+galaxy0" python_template_version="3.5" profile="21.05"> | ||||||||||
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| <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
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This can go in macros.xml. Wondering if these dependencies are already part of Kneaddata or does one explicitly need them?
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| kneaddata | |
| mkdir -p results/ | |
| kneaddata |
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| -o "output_dir" | |
| -o results/ |
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I would be in favor of removing this parameter
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| --threads "$number_threads" | |
| --processes "$number_processes" |
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| #if $trimmomatic.max_memory | |
| --max-memory "$trimmomatic.max_memory" | |
| #end if |
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perhaps adding a help tag could be beneficial?
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| <option value="s">Single read</option> | |
| <option value="p">Paired reads</option> | |
| <option value="single">Single read</option> | |
| <option value="paired">Paired reads</option> |
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| <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?
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| <when value="p"> | |
| <when value="paired"> |
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fastq and fastqsanger datatypes are different. Please prefer fastqsanger datatype
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| <param name="output_prefix" type="text" label="Custom prefix for all output files" help="Leave empty to keep the input file name."/> |
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| <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
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| <param name="max_memory" type="text" value="500m" label="Maximum memory for Trimmomatic"/> |
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Better names for option values?
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| <when value="skip"> | |
| </when> | |
| <when value="skip"/> |
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Change from_work_dir to results/...
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| <param name="number_threads" value="1"/> | |
| <param name="number_processes" value="1"/> |
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| <param name="single_read" value="28C.single.fastq"/> | |
| <param name="single_read" value="test_single.fastq"/> |
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| <output name="paired_forward" file="paired_forward.fastq"/> | |
| <output name="paired_forward" file="test_paired_1.fastq"/> |
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| <output name="paired_backward" file="paired_backward.fastq"/> | |
| <output name="paired_backward" file="test_paired_2.fastq"/> |
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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
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There was a problem hiding this comment. You can use test data for KneadData from BMTagger |
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