Mercurial > repos > ebi-gxa > seurat_export_cellbrowser
view seurat_export_cellbrowser.xml @ 5:249392cd0d99 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author | ebi-gxa |
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date | Fri, 04 Mar 2022 07:28:44 +0000 |
parents | e7d338f8c4fc |
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<tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> <description>produces files for UCSC CellBrowser import.</description> <macros> <import>seurat_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version" /> <command detect_errors="exit_code"><![CDATA[ #if $markers_file: cp '$markers_file' markers.csv; #end if seurat-export-cellbrowser.R @INPUT_OBJECT@ #if $markers_file: -m markers.csv #end if -o output_html; cd output_html && tar -cf '$output' *; ]]></command> <inputs> <expand macro="input_object_params"/> <param name="markers_file" type="data" optional="True" format="txt" label="Marker genes file from Seurat" /> </inputs> <outputs> <data name="output" format="tar" label="${tool.name} on ${on_string}: UCSC CellBrowser bundle"/> </outputs> <tests> <test> <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-tsne.rds"/> <param name="markers_file" ftype="txt" value="E-MTAB-6077-3k_features_90_cells-markers.csv"/> <output name="output" > <assert_contents> <has_size value="2182656" delta="200000"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool converts a Seurat object (hopefully with t-SNE results) and its accompanying marker genes file (optional) to a tar that can be feed to the UCSC CellBrowser tool. @SEURAT_INTRO@ ----- **Inputs** * RDS object ----- **Outputs** * Text file .. _Seurat: https://www.nature.com/articles/nbt.4096 .. _Satija Lab: https://satijalab.org/seurat/ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>