Mercurial > repos > gaelcge > cellranger_atac_galaxy

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