view seurat_select_integration_features.xml @ 0:699c0ca328f2 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6

<tool id="seurat_select_integration_features" name="Seurat select integration features" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
    <description>from a list of studies</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code"><![CDATA[
    @INPUT_OBJS_PREAMBLE@
    seurat-select-integration-features.R
    @INPUT_OBJECTS@

    --nfeatures '$nfeatures'


    #if $assay_list
    --assay-list '$assay_list'
    #end if

    $verbose


    #if $fvf_nfeatures
    --fvf-nfeatures '$fvf_nfeatures'
    #end if


    --file-out '$file_out'


    ]]></command>
    <inputs>
        <expand macro="input_object_params" multiple="True"  />
        <param label="Number of features" optional='true' value='2000' name="nfeatures" argument="--nfeatures" type="integer"   help="Number of features to return"/>
        <param label="Assay-list" optional='true' name="assay_list" argument="--assay-list" type="text"   help="Name or vector of assay names (one for each object) from which to pull the variable features."/>
        <param label="Verbose" optional='true' value='true' name="verbose" argument="--do-not-verbose" type="boolean"  truevalue='' falsevalue='--do-not-verbose' checked='true' help="Print messages"/>
        <param label="Fvf nfeatures" optional='true' value='2000' name="fvf_nfeatures" argument="--fvf-nfeatures" type="integer"   help="nfeatures for FindVariableFeatures. Used if VariableFeatures have not been set for any object in input."/>

    </inputs>
    <outputs>
        <data label="${tool.name} on ${on_string}: Rdata file with features" name="file_out" format='rdata' />
    </outputs>
    <tests>
      <!-- MANUAL TESTS -->
      <test>
        <param name="rds_seurat_file" ftype="rdata" value="ifnb_ctrl_norm_fvg.rds,ifnb_stim_norm_fvg.rds"/>
        <output name="file_out" ftype="rdata" >
          <assert_contents>
            <has_size value="9506" delta="950"/>
          </assert_contents>
        </output>
      </test>
      <!-- END MANUAL TESTS -->
    </tests>
<help>
<!-- MANUAL HELP -->
<![CDATA[
.. class:: infomark

**What it does**

@SEURAT_INTRO@

This tool aims to facilitate the first steps of the Seurat 4.0.4 https://satijalab.org/seurat/articles/integration_introduction.html
tutorial, to select features for integration of different datasets. This features can be used then with the integration tool.

All options are documented in-line.

-----

**Inputs**

* A set of Seurat objects (can be given in other formats as well) to integrate. These objects should be at least normalised and have the find variable genes/features method applied.
* All other inputs are optional (see above).

-----

**Outputs**

* A Seurat (or other format depending on selection) with the integrated object.

@VERSION_HISTORY@
]]>
<!-- END MANUAL HELP -->
</help>
    <expand macro="citations" />
</tool>