Mercurial > repos > gaelcge > cellranger_atac_galaxy
comparison tool_setup.md @ 0:a62bafb1aaf8 draft default tip
"planemo upload commit ff0d185541dc4b0a5839fca166f1beb459dee61c"
| author | gaelcge |
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| date | Tue, 02 Aug 2022 19:42:44 +0000 |
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| -1:000000000000 | 0:a62bafb1aaf8 |
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| 1 # Setup for creating a Galaxy wrapper for Cellranger-ATAC with planemo | |
| 2 | |
| 3 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 | |
| 4 | |
| 5 ## Generate galaxy tool xml using planemo tool_init | |
| 6 planemo tool_init --force \ | |
| 7 --id 'cellranger_atac' \ | |
| 8 --name 'Process 10x Genomics single-cell ATAC-seq data using CellRanger-ATAC.'\ | |
| 9 --example_command 'cellranger-atac count' \ | |
| 10 --cite_url 'https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/fastq-input#ATACIntro' \ | |
| 11 --help_from_command 'cellranger-atac' | |
| 12 | |
| 13 ## Test run with very small test data | |
| 14 cellranger-atac count --id=sample345 \ | |
| 15 --reference= \ | |
| 16 --fastqs=/home/florian/GenAP2/test_datasets/cellranger_ATAC/atac_pbmc_500_nextgem_fastqs/100k_sub \ | |
| 17 --sample=test \ | |
| 18 --localcores=2 \ | |
| 19 --localmem=6 |