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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:41:23 +0000
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1 <tool id="seurat_map_query" name="Seurat map query" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
2 <description>maps against a UMAP layout</description>
3 <macros>
4 <import>seurat_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version" />
8 <command detect_errors="exit_code"><![CDATA[
9 @REFERENCE_OBJ_PREAMBLE@
10 @ANCHORS_OBJ_PREAMBLE@
11 @QUERY_OBJ_PREAMBLE@
12 seurat-map-query.R
13 @OUTPUT_OBJECT@
14 @REFERENCE_OBJECT@
15 @ANCHORS_OBJECT@
16 @QUERY_OBJECT@
17
18 #if $refdata_field_or_assay
19 --refdata-field-or-assay 'list($refdata_field_or_assay = "$refdata_field_or_assay")'
20 #end if
21
22
23 #if $new_reduction_name
24 --new-reduction-name '$new_reduction_name'
25 #end if
26
27
28 #if $reference_reduction
29 --reference-reduction '$reference_reduction'
30 #end if
31
32
33 #if $reduction_model
34 --reduction-model '$reduction_model'
35 #end if
36
37
38 ## #if $transferdata_args
39 ## --transferdata-args '$transferdata_args'
40 ## #end if
41
42
43 ## #if $integrated_embedding_args
44 ## --integrated-embedding-args '$integrated_embedding_args'
45 ## #end if
46
47
48 ## #if $project_umap_args
49 ## --project-umap-args '$project_umap_args'
50 ## #end if
51
52
53 ]]></command>
54 <inputs>
55 <expand macro="output_object_params" />
56 <expand macro="input_object_params" varname="reference" />
57 <expand macro="input_object_params" varname="anchors" />
58 <expand macro="input_object_params" varname="query" />
59 <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.">
60 <validator type="regex" message="Value may only include R variable allowed characters: alphanumeric, underscores and period.">^[A-Za-z0-9_\.]+$</validator>
61 </param>
62 <param label="New-reduction-name" optional='true' name="new_reduction_name" argument="--new-reduction-name" type="text" help="Name for new integrated dimensional reduction."/>
63 <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"/>
64 <param label="Reduction-model" optional='true' name="reduction_model" argument="--reduction-model" type="text" help="DimReduc object name that contains the umap model"/>
65 <!-- these params could pose an injection danger and their handling should be improved before being enabled
66 <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' )"/>
67 <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' )"/>
68 <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' )"/>
69 -->
70 </inputs>
71 <outputs>
72 <expand macro="output_files"/>
73 </outputs>
74 <tests>
75 <!-- MANUAL TESTS -->
76 <test>
77 <conditional name="query">
78 <param name="rds_seurat_file" ftype="rdata" value="Classify_query.rds"/>
79 </conditional>
80 <conditional name="anchors">
81 <param name="rds_seurat_file" ftype="rdata" value="Classify_anchors.rds"/>
82 </conditional>
83 <conditional name="reference">
84 <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>
85 </conditional>
86 <param name="refdata_field_or_assay" value="celltype"/>
87
88 <output name="rds_seurat_file" ftype="rdata" >
89 <assert_contents>
90 <has_size value="48941879" delta_frac="0.1" />
91 </assert_contents>
92 </output>
93 </test>
94 <!-- END MANUAL TESTS -->
95 </tests>
96 <help>
97 <!-- MANUAL HELP -->
98 <![CDATA[
99 .. class:: infomark
100
101 **What it does**
102
103 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
104 tutorial.
105
106 It will run the MapQuery method using the query,
107 anchors object and reference used to calculate the anchors. All
108 options are documented in-line.
109
110 -----
111
112 **Inputs**
113
114 * Query object (can be specified in different formats)
115 * Anchors object (can be specified in different formats)
116 * Reference object (can be specified in different formats)
117
118 All the rest of the parameters are optional.
119
120 -----
121
122 **Outputs**
123
124 * A Seurat (or other format depending on selection) with the mapped object.
125
126 ]]>
127 <!-- END MANUAL HELP -->
128 </help>
129 <expand macro="citations" />
130 </tool>