annotate seurat_filter_cells.xml @ 0:c1848daebad1 draft

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

<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 [e-mail], 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>