Mercurial > repos > ebi-gxa > seurat_filter_cells
diff seurat_filter_cells.xml @ 0:c1848daebad1 draft
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 11:16:07 -0400 |
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children | 30982e805f8c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_filter_cells.xml Wed Apr 03 11:16:07 2019 -0400 @@ -0,0 +1,84 @@ +<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>