Mercurial > repos > ebi-gxa > seurat_select_integration_features

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:40:57 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:699c0ca328f2
1 <tool id="seurat_select_integration_features" name="Seurat select integration features" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
2 <description>from a list of studies</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 @INPUT_OBJS_PREAMBLE@
10 seurat-select-integration-features.R
11 @INPUT_OBJECTS@
12
13 --nfeatures '$nfeatures'
14
15
16 #if $assay_list
17 --assay-list '$assay_list'
18 #end if
19
20 $verbose
21
22
23 #if $fvf_nfeatures
24 --fvf-nfeatures '$fvf_nfeatures'
25 #end if
26
27
28 --file-out '$file_out'
29
30
31 ]]></command>
32 <inputs>
33 <expand macro="input_object_params" multiple="True" />
34 <param label="Number of features" optional='true' value='2000' name="nfeatures" argument="--nfeatures" type="integer" help="Number of features to return"/>
35 <param label="Assay-list" optional='true' name="assay_list" argument="--assay-list" type="text" help="Name or vector of assay names (one for each object) from which to pull the variable features."/>
36 <param label="Verbose" optional='true' value='true' name="verbose" argument="--do-not-verbose" type="boolean" truevalue='' falsevalue='--do-not-verbose' checked='true' help="Print messages"/>
37 <param label="Fvf nfeatures" optional='true' value='2000' name="fvf_nfeatures" argument="--fvf-nfeatures" type="integer" help="nfeatures for FindVariableFeatures. Used if VariableFeatures have not been set for any object in input."/>
38
39 </inputs>
40 <outputs>
41 <data label="${tool.name} on ${on_string}: Rdata file with features" name="file_out" format='rdata' />
42 </outputs>
43 <tests>
44 <!-- MANUAL TESTS -->
45 <test>
46 <param name="rds_seurat_file" ftype="rdata" value="ifnb_ctrl_norm_fvg.rds,ifnb_stim_norm_fvg.rds"/>
47 <output name="file_out" ftype="rdata" >
48 <assert_contents>
49 <has_size value="9506" delta="950"/>
50 </assert_contents>
51 </output>
52 </test>
53 <!-- END MANUAL TESTS -->
54 </tests>
55 <help>
56 <!-- MANUAL HELP -->
57 <![CDATA[
58 .. class:: infomark
59
60 **What it does**
61
62 @SEURAT_INTRO@
63
64 This tool aims to facilitate the first steps of the Seurat 4.0.4 https://satijalab.org/seurat/articles/integration_introduction.html
65 tutorial, to select features for integration of different datasets. This features can be used then with the integration tool.
66
67 All options are documented in-line.
68
69 -----
70
71 **Inputs**
72
73 * 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.
74 * All other inputs are optional (see above).
75
76 -----
77
78 **Outputs**
79
80 * A Seurat (or other format depending on selection) with the integrated object.
81
82 @VERSION_HISTORY@
83 ]]>
84 <!-- END MANUAL HELP -->
85 </help>
86 <expand macro="citations" />
87 </tool>