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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:13 +0000
parents 970696a7ae0b
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0:970696a7ae0b 1:834f7d8e5b4c
1 <tool id="seurat_convert" name="Seurat 3 converter" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> 1 <tool id="seurat_convert" name="Seurat 4 converter" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
2 <description>translates different single cell formats</description> 2 <description>translates different single cell formats</description>
3 <macros> 3 <macros>
4 <import>seurat_macros.xml</import> 4 <import>seurat_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version" /> 7 <expand macro="version" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @INPUT_OBJ_PREAMBLE@
9 seurat-convert.R 10 seurat-convert.R
10 @INPUT_OBJECT@ 11 @INPUT_OBJECT@
11 @OUTPUT_OBJECT@ 12 @OUTPUT_OBJECT@
12 ]]></command> 13 ]]></command>
13 <inputs> 14 <inputs>
74 <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5ad"/> 75 <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5ad"/>
75 </conditional> 76 </conditional>
76 <param name="format" value="rds_seurat"/> 77 <param name="format" value="rds_seurat"/>
77 <output name="rds_seurat_file"> 78 <output name="rds_seurat_file">
78 <assert_contents> 79 <assert_contents>
79 <has_size value="2965562" delta="200000"/> 80 <has_size value="3761959" delta="200000"/>
80 </assert_contents> 81 </assert_contents>
81 </output> 82 </output>
82 </test> 83 </test>
84 <!-- <test>
85 <conditional name="input">
86 <param name="format" value="anndata"/>
87 <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells_sc182.h5ad" ftype="h5ad"/>
88 </conditional>
89 <param name="format" value="rds_seurat"/>
90 <output name="rds_seurat_file">
91 <assert_contents>
92 <has_size value="3761959" delta="200000"/>
93 </assert_contents>
94 </output>
95 </test> -->
96
83 </tests> 97 </tests>
84 <help><![CDATA[ 98 <help><![CDATA[
85 .. class:: infomark 99 .. class:: infomark
86 100
87 **What it does** 101 **What it does**
88 102
89 This tool uses Seurat 3 to convert formats. Possible inputs are: 103 @SEURAT_INTRO@
90 104
91 * Seurat 3 105 This tool uses Seurat 4 to convert formats. Possible inputs are:
92 * Loom (probably earlier than Loom 3.0) 106
93 * AnnData (contemporary versions to Seurat 3, most likely up to AnnData 0.6.22.post1) 107 * Seurat 3/4
108 * Loom (versions contemporary to Seurat 4)
109 * AnnData (contemporary versions to Seurat 4)
94 * Single Cell Experiment 110 * Single Cell Experiment
95 111
96 Possible outputs are: 112 Possible outputs are:
97 113
98 * Seurat 3 114
99 * Loom (as produced by loomR package) 115 * Seurat 4
116 * Loom
100 * Single Cell Experiment 117 * Single Cell Experiment
101 118
102 For newer versions of AnnData and Loom, please try the Seurat 4 version of this tool. 119 For newer versions of AnnData and Loom, please try the Seurat 4 version of this tool.
103
104 @SEURAT_INTRO@
105 120
106 121
107 .. _Seurat: https://www.nature.com/articles/nbt.4096 122 .. _Seurat: https://www.nature.com/articles/nbt.4096
108 .. _Satija Lab: https://satijalab.org/seurat/ 123 .. _Satija Lab: https://satijalab.org/seurat/
109 124