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comparison seurat_convert.xml @ 0:970696a7ae0b draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:28:21 +0000
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children 834f7d8e5b4c
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-1:000000000000 0:970696a7ae0b
1 <tool id="seurat_convert" name="Seurat 3 converter" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
2 <description>translates different single cell formats</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 seurat-convert.R
10 @INPUT_OBJECT@
11 @OUTPUT_OBJECT@
12 ]]></command>
13 <inputs>
14 <expand macro="input_object_params"/>
15 <expand macro="output_object_params"/>
16 </inputs>
17
18 <outputs>
19 <expand macro="output_files"/>
20 </outputs>
21
22 <tests>
23 <test>
24 <conditional name="input">
25 <param name="format" value="rds_seurat"/>
26 <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
27 </conditional>
28 <param name="format" value="loom"/>
29 <output name="loom_file">
30 <assert_contents>
31 <has_h5_keys keys="layers,matrix,row_attrs"/>
32 </assert_contents>
33 </output>
34 </test>
35 <test>
36 <conditional name="input">
37 <param name="format" value="rds_seurat"/>
38 <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
39 </conditional>
40 <param name="format" value="rds_sce"/>
41 <output name="rds_sce_file">
42 <assert_contents>
43 <has_size value="2368166" delta="200000"/>
44 </assert_contents>
45 </output>
46 </test>
47 <test>
48 <conditional name="input">
49 <param name="format" value="loom"/>
50 <param name="loom_file" value="E-MTAB-6077-3k_features_90_cells_loom.h5" ftype="h5"/>
51 </conditional>
52 <param name="format" value="rds_sce"/>
53 <output name="rds_sce_file">
54 <assert_contents>
55 <has_size value="2432700" delta="200000"/>
56 </assert_contents>
57 </output>
58 </test>
59 <test>
60 <conditional name="input">
61 <param name="format" value="rds_sce"/>
62 <param name="rds_sce_file" value="E-MTAB-6077-3k_features_90_cells_sce.rds" ftype="rdata.sce"/>
63 </conditional>
64 <param name="format" value="rds_seurat"/>
65 <output name="rds_seurat_file">
66 <assert_contents>
67 <has_size value="2366603" delta="200000"/>
68 </assert_contents>
69 </output>
70 </test>
71 <test>
72 <conditional name="input">
73 <param name="format" value="anndata"/>
74 <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5ad"/>
75 </conditional>
76 <param name="format" value="rds_seurat"/>
77 <output name="rds_seurat_file">
78 <assert_contents>
79 <has_size value="2965562" delta="200000"/>
80 </assert_contents>
81 </output>
82 </test>
83 </tests>
84 <help><![CDATA[
85 .. class:: infomark
86
87 **What it does**
88
89 This tool uses Seurat 3 to convert formats. Possible inputs are:
90
91 * Seurat 3
92 * Loom (probably earlier than Loom 3.0)
93 * AnnData (contemporary versions to Seurat 3, most likely up to AnnData 0.6.22.post1)
94 * Single Cell Experiment
95
96 Possible outputs are:
97
98 * Seurat 3
99 * Loom (as produced by loomR package)
100 * Single Cell Experiment
101
102 For newer versions of AnnData and Loom, please try the Seurat 4 version of this tool.
103
104 @SEURAT_INTRO@
105
106
107 .. _Seurat: https://www.nature.com/articles/nbt.4096
108 .. _Satija Lab: https://satijalab.org/seurat/
109
110 @VERSION_HISTORY@
111
112 ]]></help>
113 <expand macro="citations" />
114 </tool>