comparison seurat_filter_cells.xml @ 1:30982e805f8c draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f

0:c1848daebad1

<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**

1:30982e805f8c

<tool id="seurat_filter_cells" name="Seurat FilterCells" version="@SEURAT_VERSION@_@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 [e-mail], 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="input" ftype="rdata" value="seurat.rds"/>
            <output name="rds_seurat_file" ftype="rdata" value="out_filter.rds" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool filters cells in a Seurat object.

@SEURAT_INTRO@

-----

**Inputs**