annotate seurat_map_query.xml @ 0:d2f61c442910 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6

<tool id="seurat_map_query" name="Seurat map query" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
    <description>maps against a UMAP layout</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code"><![CDATA[
    @REFERENCE_OBJ_PREAMBLE@
    @ANCHORS_OBJ_PREAMBLE@
    @QUERY_OBJ_PREAMBLE@
    seurat-map-query.R
    @OUTPUT_OBJECT@
    @REFERENCE_OBJECT@
    @ANCHORS_OBJECT@
    @QUERY_OBJECT@

    #if $refdata_field_or_assay
    --refdata-field-or-assay 'list($refdata_field_or_assay = "$refdata_field_or_assay")'
    #end if


    #if $new_reduction_name
    --new-reduction-name '$new_reduction_name'
    #end if


    #if $reference_reduction
    --reference-reduction '$reference_reduction'
    #end if


    #if $reduction_model
    --reduction-model '$reduction_model'
    #end if


    ## #if $transferdata_args
    ## --transferdata-args '$transferdata_args'
    ## #end if


    ## #if $integrated_embedding_args
    ## --integrated-embedding-args '$integrated_embedding_args'
    ## #end if


    ## #if $project_umap_args
    ## --project-umap-args '$project_umap_args'
    ## #end if


    ]]></command>
    <inputs>
        <expand macro="output_object_params" />
        <expand macro="input_object_params" varname="reference"  />
        <expand macro="input_object_params" varname="anchors"  />
        <expand macro="input_object_params" varname="query"  />
        <param label="Refdata-field-or-assay" optional='true' name="refdata_field_or_assay" argument="--refdata-field-or-assay" type="text"   help="The name of the metadata field or assay from the reference object provided. This requires the reference parameter to be specified.">
          <validator type="regex" message="Value may only include R variable allowed characters: alphanumeric, underscores and period.">^[A-Za-z0-9_\.]+$</validator>
        </param>
        <param label="New-reduction-name" optional='true' name="new_reduction_name" argument="--new-reduction-name" type="text"   help="Name for new integrated dimensional reduction."/>
        <param label="Reference-reduction" optional='true' name="reference_reduction" argument="--reference-reduction" type="text"   help="Name of reduction to use from the reference for neighbor finding"/>
        <param label="Reduction-model" optional='true' name="reduction_model" argument="--reduction-model" type="text"   help="DimReduc object name that contains the umap model"/>
        <!-- these params could pose an injection danger and their handling should be improved before being enabled 
          <param label="Transferdata-args" optional='true' name="transferdata_args" argument="transferdata-args" type="text"   help="A named list of additional arguments to TransferData, written in R syntax .ie list( argument = 'value' )"/>
          <param label="Integrated-embedding-args" optional='true' name="integrated_embedding_args" argument="integrated-embedding-args" type="text"   help="A named list of additional arguments to IntegrateEmbeddings, written in R syntax .ie list( argument = 'value' )"/>
          <param label="Project-umap-args" optional='true' name="project_umap_args" argument="project-umap-args" type="text"   help="A named list of additional arguments to ProjectUMAP, written in R syntax .ie list( argument = 'value' )"/>
        -->
    </inputs>
    <outputs>
        <expand macro="output_files"/>
    </outputs>
    <tests>
      <!-- MANUAL TESTS -->
      <test>
        <conditional name="query">
          <param name="rds_seurat_file" ftype="rdata" value="Classify_query.rds"/>
        </conditional>
        <conditional name="anchors">
          <param name="rds_seurat_file" ftype="rdata" value="Classify_anchors.rds"/>
        </conditional>
        <conditional name="reference">
          <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>
        </conditional>
        <param name="refdata_field_or_assay" value="celltype"/>

        <output name="rds_seurat_file" ftype="rdata" >
          <assert_contents>
            <has_size value="48941879" delta_frac="0.1" />
          </assert_contents>
        </output>
      </test>
      <!-- END MANUAL TESTS -->
    </tests>
<help>
<!-- MANUAL HELP -->
<![CDATA[
.. class:: infomark

**What it does**

This tool aims to facilitate the mapping steps to UMAP of the Seurat 4.0.4 https://satijalab.org/seurat/articles/integration_mapping.html#unimodal-umap-projection
tutorial.

It will run the MapQuery method using the query,
anchors object and reference used to calculate the anchors. All
options are documented in-line.

-----

**Inputs**

* Query object (can be specified in different formats)
* Anchors object (can be specified in different formats)
* Reference object (can be specified in different formats)

All the rest of the parameters are optional.

-----

**Outputs**

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

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