Mercurial > repos > ebi-gxa > seurat_create_seurat_object
diff seurat_create_object.xml @ 0:f8865ae30723 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:19:37 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_create_object.xml Wed Apr 03 11:19:37 2019 -0400 @@ -0,0 +1,60 @@ +<tool id="seurat_create_seurat_object" name="Seurat CreateSeuratObject" version="2.3.1+galaxy0"> + <description>create a Seurat object</description> + <macros> + <import>seurat_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version" /> + <command detect_errors="exit_code"><![CDATA[ +seurat-create-seurat-object.R + +--input-object-file '$input' +--output-object-file '$output' +]]></command> + + <inputs> + <param name="input" type="data" format="rdata" label="Seurat object" help="RDS file from Seurat read10x module." /> + </inputs> + + <outputs> + <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> + </outputs> + + <tests> + <test> + <param name="input" ftype="rdata" value="deng.rds"/> + <output name="output" ftype="rdata" value="seurat.rds" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. +It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and +interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse +types of single cell data. + +This tool creates a Seurat object from an RDS object. + +----- + +**Inputs** + + * RDS object from Seurat read_10x module. + +----- + +**Outputs** + + * Seurat RDS object + +.. _Seurat: https://www.nature.com/articles/nbt.4096 +.. _Satija Lab: https://satijalab.org/seurat/ + +@VERSION_HISTORY@ + +]]></help> + <expand macro="citations" /> +</tool>