Mercurial > repos > iuc > mudata_import_export

annotate mudata_import_export.xml @ 4:aa9162c059b3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon commit fef10e0d450018d1e6ba4cbbda76c7686edc8aae
author iuc
date Sat, 25 Oct 2025 21:00:59 +0000
parents 089a6101d5d9
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089a6101d5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/muon/ commit bcf2ec32c3d13b29da55e0e638da7ddd7162c436
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1 <tool id="mudata_import_export" name="MuData import and export" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="bio_tools"/>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @CMD@
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="script_file"><![CDATA[
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13 @CMD_imports@
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14 #if $operation.mode == 'import'
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15 import anndata as ad
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16
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17 mdata = mu.MuData({
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18 #for $modality in $operation.modalities
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19 '$modality.name': ad.read_h5ad('$modality.anndata'),
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20 #end for
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21 })
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22 #if $make_unique
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23 mdata.var_names_make_unique()
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24 #end if
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25 mdata.write_h5mu('mudata.h5mu')
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26
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27 #else if $operation.mode == 'export'
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28 mdata = mu.read_h5mu('$operation.mudata_in')
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29 for mod in mdata.mod:
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30 mdata[mod].write_h5ad(mod + '.h5ad')
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31
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32 #end if
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33
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34 ]]></configfile>
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35 </configfiles>
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36 <inputs>
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37 <conditional name="operation">
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38 <param name="mode" type="select" label="Mode of operation">
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39 <option value="import" selected="true">Import multiple Anndata objects into a MuData object</option>
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40 <option value="export">Export Anndata objects from a MuData objects</option>
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41 </param>
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42 <when value="import">
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43 <repeat name="modalities" title="Modalities" min="2" default="2">
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44 <param name="name" type="text" label="Modality name" value=""
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45 help="Name to give for the modality in the MuData object">
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46 <expand macro="sanitize_string" />
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47 </param>
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48 <param name="anndata" type="data" format="h5ad" label="Anndata object for the modality"/>
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49 </repeat>
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50 <param name="make_unique" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make variable names unique?"/>
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51 </when>
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52 <when value="export">
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53 <param name="mudata_in" type="data" format="h5ad" label="Multimodal MuData object"/>
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54 </when>
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55 </conditional>
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56 <expand macro="inputs_common_advanced" />
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57 </inputs>
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58 <outputs>
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59 <data name="mudata_out" format="h5ad" from_work_dir="mudata.h5mu" label="MuData object built from ${on_string}">
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60 <filter>operation['mode'] == 'import' </filter>
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61 </data>
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62 <collection name="collection_anndata" type="list" label="Anndata objects extracted from ${on_string}">
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63 <discover_datasets pattern="(?P&lt;designation&gt;.*).h5ad" format="h5ad"/>
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64 <filter>operation['mode'] == 'export' </filter>
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65 </collection>
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66 <expand macro="outputs_common_advanced"/>
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67 </outputs>
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68 <tests>
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69 <test expect_num_outputs="2">
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70 <!--Import test for RNA and ATAC modalities-->
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71 <conditional name="operation">
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72 <param name="mode" value="import"/>
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73 <repeat name="modalities">
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74 <param name="name" value="RNA"/>
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75 <param name="anndata" location="https://zenodo.org/records/12570984/files/rna.h5ad"/>
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76 </repeat>
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77 <repeat name="modalities">
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78 <param name="name" value="ATAC"/>
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79 <param name="anndata" location="https://zenodo.org/records/12570984/files/atac.h5ad"/>
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80 </repeat>
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81 <param name="make_unique" value="True"/>
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82 </conditional>
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83 <section name="advanced_common">
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84 <param name="show_log" value="true" />
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85 </section>
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86 <output name="hidden_output">
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87 <assert_contents>
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88 <has_text_matching expression="mu.MuData"/>
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89 <has_text_matching expression="'RNA': ad.read"/>
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90 <has_text_matching expression="'ATAC': ad.read"/>
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91 <has_text_matching expression="var_names_make_unique()"/>
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92 </assert_contents>
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93 </output>
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94 <output name="mudata_out" ftype="h5ad">
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95 <assert_contents>
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96 <has_h5_keys keys="mod/RNA"/>
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97 <has_h5_keys keys="mod/ATAC"/>
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98 <has_h5_keys keys="var/feature_types"/>
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99 </assert_contents>
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100 </output>
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101 </test>
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102 <test expect_num_outputs="2">
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103 <!--Export test for RNA and ATAC modalities-->
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104 <conditional name="operation">
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105 <param name="mode" value="export"/>
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106 <param name="mudata_in" location="https://zenodo.org/records/12570984/files/rna_atac.h5mu"/>
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107 </conditional>
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108 <section name="advanced_common">
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109 <param name="show_log" value="true" />
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110 </section>
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111 <output name="hidden_output">
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112 <assert_contents>
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113 <has_text_matching expression="mu.read_h5mu"/>
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114 <has_text_matching expression="write_h5ad"/>
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115 </assert_contents>
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116 </output>
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117 <output_collection name="collection_anndata" type="list" count="2">
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118 <element name="ATAC" ftype="h5ad">
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119 <assert_contents>
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120 <has_h5_keys keys="var/gene_ids"/>
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121 <has_h5_keys keys="uns/neighbors"/>
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122 <has_h5_keys keys="obsp/connectivities"/>
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123 </assert_contents>
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124 </element>
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125 <element name="RNA" ftype="h5ad">
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126 <assert_contents>
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127 <has_h5_keys keys="var/gene_ids"/>
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128 <has_h5_keys keys="uns/neighbors"/>
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129 <has_h5_keys keys="obsp/connectivities"/>
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130 </assert_contents>
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131 </element>
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132 </output_collection>
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136 **What it does**
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137 Create MuData from AnnData is a tool that allows creating a muon.MuData object out of two or more AnnData objects
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138 for multimodal analysis. The multimodal data is created by combining AnnData objects as
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139 h5ad files into a MuData object as a h5mu file using muon.
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140 Furthermore, it runs pp.intersect_obs to keep only entries present in both modalities (AnnData objects) in the
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141 final MuData file.
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142 ]]></help>
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143 <expand macro="citations"/>
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144 </tool>