Mercurial > repos > ebi-gxa > seurat_filter_cells
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
author | ebi-gxa |
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date | Wed, 13 Mar 2019 12:50:47 -0400 |
parents | eb20971d191c |
children | 040ab5587f2a |
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<tool id="seurat_filter_cells" name="Seurat FilterCells" version="2.3.1+galaxy1"> <description>filter cells in a Seurat object</description> <macros> <import>seurat_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version" /> <command detect_errors="exit_code"><![CDATA[ seurat-filter-cells.R --input-object-file '$input' #if $subset: --subset-names '$subset' #else --subset-names nUMI #end if #if $low: --low-thresholds $low #end if #if $high: --high-thresholds $high #end if #if $cells: --cells-use $cells #end if --output-object-file '$output' ]]></command> <inputs> <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Output from Seurat create object." /> <param name="subset" argument="--subset-names" type="text" label="Subset names" optional="True" help="Parameters to subset on. Eg, the name of a gene, PC1, a column name in object@meta.data, etc. Any argument that can be retreived using FetchData. Multiple values can be separated by colons (:)."> <validator type="regex" message="Please only use letters or numbers">^[\(\w\)]+$</validator> </param> <param name="low" argument="--low-thresholds" type="float" optional="True" label="Low threshold for filtering cells" help="Multiple values can be separated by colons (:) and should have same length as provided for `Subset names`." /> <param name="high" argument="--high-thresholds" type="float" optional="True" label="High threshold for filtering cells" help="Multiple values can be separated by colons (:) and should have same length as provided for `Subset names`." /> <param name="cells" argument="--cells-use" type="text" min="0" optional="True" help="Comma-separated list of cell names to use as a subset." label="Cells to use" /> </inputs> <outputs> <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> </outputs> <tests> <test> <param name="input" ftype="rdata" value="seurat.rds"/> <output name="output" ftype="rdata" value="out_filter.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 filters a Seurat RDS object. ----- **Inputs** * Seurat RDS object. Probably the one produced by Seurat create object. * Subset names. A list of attributes to subset on, colon separated (:). * Low thresholds. A minimum value for each of the attributes set in subset names, again, colon separated (:). Optional. * High thresholds. A maximum value for each of the attributes set in subset names, again, colon separated (:). Optional. * Cells to use. A list of cell names/idenfifiers to filter positively by. ----- **Outputs** * Seurat RDS object filtered according to the inputs. .. _Seurat: https://www.nature.com/articles/nbt.4096 .. _Satija Lab: https://satijalab.org/seurat/ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>