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author | ebi-gxa |
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date | Sat, 02 Mar 2024 10:41:23 +0000 |
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<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>