Mercurial > repos > ebi-gxa > seurat_convert

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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:13 +0000
parents 970696a7ae0b
children
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834f7d8e5b4c planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
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1 <tool id="seurat_convert" name="Seurat 4 converter" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
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2 <description>translates different single cell formats</description>
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3 <macros>
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4 <import>seurat_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @INPUT_OBJ_PREAMBLE@
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10 seurat-convert.R
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11 @INPUT_OBJECT@
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12 @OUTPUT_OBJECT@
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13 ]]></command>
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14 <inputs>
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15 <expand macro="input_object_params"/>
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16 <expand macro="output_object_params"/>
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17 </inputs>
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18
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19 <outputs>
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20 <expand macro="output_files"/>
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21 </outputs>
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22
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23 <tests>
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24 <test>
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25 <conditional name="input">
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26 <param name="format" value="rds_seurat"/>
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27 <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
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28 </conditional>
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29 <param name="format" value="loom"/>
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30 <output name="loom_file">
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31 <assert_contents>
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32 <has_h5_keys keys="layers,matrix,row_attrs"/>
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33 </assert_contents>
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34 </output>
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35 </test>
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36 <test>
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37 <conditional name="input">
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38 <param name="format" value="rds_seurat"/>
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39 <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
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40 </conditional>
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41 <param name="format" value="rds_sce"/>
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42 <output name="rds_sce_file">
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43 <assert_contents>
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44 <has_size value="2368166" delta="200000"/>
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45 </assert_contents>
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46 </output>
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47 </test>
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48 <test>
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49 <conditional name="input">
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50 <param name="format" value="loom"/>
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51 <param name="loom_file" value="E-MTAB-6077-3k_features_90_cells_loom.h5" ftype="h5"/>
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52 </conditional>
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53 <param name="format" value="rds_sce"/>
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54 <output name="rds_sce_file">
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55 <assert_contents>
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56 <has_size value="2432700" delta="200000"/>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 <test>
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61 <conditional name="input">
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62 <param name="format" value="rds_sce"/>
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63 <param name="rds_sce_file" value="E-MTAB-6077-3k_features_90_cells_sce.rds" ftype="rdata.sce"/>
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64 </conditional>
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65 <param name="format" value="rds_seurat"/>
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66 <output name="rds_seurat_file">
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67 <assert_contents>
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68 <has_size value="2366603" delta="200000"/>
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test>
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73 <conditional name="input">
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74 <param name="format" value="anndata"/>
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75 <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5ad"/>
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76 </conditional>
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77 <param name="format" value="rds_seurat"/>
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78 <output name="rds_seurat_file">
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79 <assert_contents>
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80 <has_size value="3761959" delta="200000"/>
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <!-- <test>
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85 <conditional name="input">
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86 <param name="format" value="anndata"/>
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87 <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells_sc182.h5ad" ftype="h5ad"/>
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88 </conditional>
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89 <param name="format" value="rds_seurat"/>
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90 <output name="rds_seurat_file">
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91 <assert_contents>
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92 <has_size value="3761959" delta="200000"/>
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93 </assert_contents>
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94 </output>
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95 </test> -->
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96
0
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97 </tests>
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98 <help><![CDATA[
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99 .. class:: infomark
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100
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101 **What it does**
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102
1
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103 @SEURAT_INTRO@
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104
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105 This tool uses Seurat 4 to convert formats. Possible inputs are:
0
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106
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107 * Seurat 3/4
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108 * Loom (versions contemporary to Seurat 4)
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109 * AnnData (contemporary versions to Seurat 4)
0
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110 * Single Cell Experiment
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111
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112 Possible outputs are:
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113
1
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114
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115 * Seurat 4
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116 * Loom
0
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117 * Single Cell Experiment
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118
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119 For newer versions of AnnData and Loom, please try the Seurat 4 version of this tool.
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120
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121
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122 .. _Seurat: https://www.nature.com/articles/nbt.4096
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123 .. _Satija Lab: https://satijalab.org/seurat/
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124
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125 @VERSION_HISTORY@
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126
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127 ]]></help>
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128 <expand macro="citations" />
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129 </tool>