view seurat_export_cellbrowser.xml @ 0:8c2b1d2659df draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4

<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>