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"planemo upload commit ff0d185541dc4b0a5839fca166f1beb459dee61c"
author | gaelcge |
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date | Tue, 02 Aug 2022 19:42:44 +0000 |
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# Setup for creating a Galaxy wrapper for Cellranger-ATAC with planemo Make sure you have a working planemo installation. To find out how to install planemo, check here: https://planemo.readthedocs.io/en/latest/installation.html ## Generate galaxy tool xml using planemo tool_init planemo tool_init --force \ --id 'cellranger_atac' \ --name 'Process 10x Genomics single-cell ATAC-seq data using CellRanger-ATAC.'\ --example_command 'cellranger-atac count' \ --cite_url 'https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/fastq-input#ATACIntro' \ --help_from_command 'cellranger-atac' ## Test run with very small test data cellranger-atac count --id=sample345 \ --reference= \ --fastqs=/home/florian/GenAP2/test_datasets/cellranger_ATAC/atac_pbmc_500_nextgem_fastqs/100k_sub \ --sample=test \ --localcores=2 \ --localmem=6