Mercurial > repos > ebi-gxa > seurat_map_query

annotate seurat_map_query.xml @ 0:9a68428ae952 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
author ebi-gxa
date Sun, 01 Oct 2023 09:06:00 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
1 <tool id="seurat_map_query" name="Seurat map query" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
2 <description>maps against a UMAP layout</description>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
3 <macros>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
4 <import>seurat_macros.xml</import>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
5 </macros>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
7 <expand macro="version" />
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
9 @REFERENCE_OBJ_PREAMBLE@
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
10 @ANCHORS_OBJ_PREAMBLE@
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
11 @QUERY_OBJ_PREAMBLE@
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
12 seurat-map-query.R
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
13 @OUTPUT_OBJECT@
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
14 @REFERENCE_OBJECT@
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
15 @ANCHORS_OBJECT@
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
16 @QUERY_OBJECT@
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
17
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
18 #if $refdata_field_or_assay
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
19 --refdata-field-or-assay '$refdata_field_or_assay'
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
20 #end if
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
21
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
22
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
23 #if $new_reduction_name
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
24 --new-reduction-name '$new_reduction_name'
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
25 #end if
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
26
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
27
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
28 #if $reference_reduction
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
29 --reference-reduction '$reference_reduction'
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
30 #end if
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
31
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
32
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
33 #if $reduction_model
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
34 --reduction-model '$reduction_model'
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
35 #end if
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
36
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
37
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
38 ## #if $transferdata_args
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
39 ## --transferdata-args '$transferdata_args'
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
40 ## #end if
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
41
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
42
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
43 ## #if $integrated_embedding_args
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
44 ## --integrated-embedding-args '$integrated_embedding_args'
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
45 ## #end if
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
46
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
47
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
48 ## #if $project_umap_args
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
49 ## --project-umap-args '$project_umap_args'
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
50 ## #end if
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
51
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
52
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
53 ]]></command>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
54 <inputs>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
55 <expand macro="output_object_params" />
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
56 <expand macro="input_object_params" varname="reference" />
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
57 <expand macro="input_object_params" varname="anchors" />
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
58 <expand macro="input_object_params" varname="query" />
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
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.">
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
60 <validator type="regex" message="Value may only include R variable allowed characters: alphanumeric, underscores and period.">^[A-Za-z0-9_\.]+$</validator>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
61 </param>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
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."/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
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"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
64 <param label="Reduction-model" optional='true' name="reduction_model" argument="--reduction-model" type="text" help="DimReduc object name that contains the umap model"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
65 <!-- these params could pose an injection danger and their handling should be improved before being enabled
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
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' )"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
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' )"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
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' )"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
69 -->
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
70 </inputs>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
71 <outputs>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
72 <expand macro="output_files"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
73 </outputs>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
74 <tests>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
75 <!-- MANUAL TESTS -->
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
76 <test>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
77 <conditional name="query">
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
78 <param name="rds_seurat_file" ftype="rdata" value="Classify_query.rds"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
79 </conditional>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
80 <conditional name="anchors">
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
81 <param name="rds_seurat_file" ftype="rdata" value="Classify_anchors.rds"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
82 </conditional>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
83 <conditional name="reference">
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
84 <param name="rds_seurat_file" ftype="rdata" value="Classify_reference.rds"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
85 </conditional>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
86
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
87 <output name="rds_seurat_file" ftype="rdata" >
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
88 <assert_contents>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
89 <has_size value="103786543" delta="10000000"/>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
90 </assert_contents>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
91 </output>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
92 </test>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
93 <!-- END MANUAL TESTS -->
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
94 </tests>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
95 <help>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
96 <!-- MANUAL HELP -->
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
97 <![CDATA[
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
98 .. class:: infomark
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
99
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
100 **What it does**
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
101
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
102 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
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
103 tutorial.
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
104
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
105 It will run the MapQuery method using the query,
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
106 anchors object and reference used to calculate the anchors. All
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
107 options are documented in-line.
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
108
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
109 -----
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
110
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
111 **Inputs**
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
112
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
113 * Query object (can be specified in different formats)
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
114 * Anchors object (can be specified in different formats)
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
115 * Reference object (can be specified in different formats)
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
116
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
117 All the rest of the parameters are optional.
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
118
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
119 -----
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
120
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
121 **Outputs**
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
122
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
123 * A Seurat (or other format depending on selection) with the mapped object.
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
124
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
125 ]]>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
126 <!-- END MANUAL HELP -->
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
127 </help>
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
128 <expand macro="citations" />
9a68428ae952 planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
ebi-gxa
parents:
diff changeset
129 </tool>