Mercurial > repos > ebi-gxa > seurat_export_cellbrowser
diff seurat_export_cellbrowser.xml @ 0:8c2b1d2659df 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 11:16:38 -0400 |
parents | |
children | 80eec773c961 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_export_cellbrowser.xml Wed Apr 03 11:16:38 2019 -0400 @@ -0,0 +1,71 @@ +<tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" version="2.3.1+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 -i '$rds_input' + +#if $markers_file: +-m markers.csv +#end if + +-o output_html; + +cd output_html && tar -cf '$output' *; +]]></command> + + <inputs> + <param name="rds_input" type="data" format="rdata" label="Seurat RDS object" /> + <param name="markers_file" type="data" 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_input" ftype="rdata" value="out_runtsne.rds"/> + <param name="markers_file" ftype="txt" value="out_markers.csv"/> + <output name="output" ftype="tar" value="out_cellbrowser_bundle.tar"/> + </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 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. +----- + +**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>