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author | ebi-gxa |
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date | Sat, 02 Mar 2024 10:40:32 +0000 |
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<tool id="seurat_filter_cells" name="Seurat FilterCells" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> <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@ #if $subsets: #set subsets_clause = ','.join(['{name}'.format(**$s) for $s in $subsets]) #set low_clause = ",".join(['{min}'.format(**$s) for $s in $subsets]) #set high_clause = ",".join(['{max}'.format(**$s) for $s in $subsets]) --subset-names '${subsets_clause}' --low-thresholds '${low_clause}' --high-thresholds '${high_clause}' #end if #if $cells: --cells-use $cells #end if @OUTPUT_OBJECT@ ]]></command> <inputs> <expand macro="input_object_params"/> <repeat name="subsets" title="Subsets used to filter cells" min="1"> <param name="name" argument="--subset-names" type="text" label="Name of parameter to filter on" help="for example nCount_RNA, nFeature_RNA, the name of a gene, PC1, a column name in object@meta.data, etc. Any argument that can be retreived using FetchData."> <validator type="regex" message="Please only use letters or numbers">^[\(\w\)]+$</validator> <option value="nCount_RNA">nCount_RNA</option> <option value="nFeature_RNA">nFeature_RNA</option> </param> <param name="min" type="float" value="0" min="0" label="Min value"/> <param name="max" type="float" value="1e9" label="Max value"/> </repeat> <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" /> <expand macro="output_object_params"/> </inputs> <outputs> <expand macro="output_files"/> </outputs> <tests> <test> <param name="name" value="nCount_RNA" /> <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells.rds" /> <output name="rds_seurat_file" ftype="rdata"> <assert_contents> <has_size value="2260044" delta="200000"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool filters cells in a Seurat object. @SEURAT_INTRO@ ----- **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>