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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 21:00:32 +0000
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-1:000000000000 0:f5672da27c4b
1 <tool id="mudata_import_export" name="MuData import and export" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="bio_tools"/>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[
9 @CMD@
10 ]]></command>
11 <configfiles>
12 <configfile name="script_file"><![CDATA[
13 @CMD_imports@
14 #if $operation.mode == 'import'
15 import anndata as ad
16
17 mdata = mu.MuData({
18 #for $modality in $operation.modalities
19 '$modality.name': ad.read_h5ad('$modality.anndata'),
20 #end for
21 })
22 #if $make_unique
23 mdata.var_names_make_unique()
24 #end if
25 mdata.write_h5mu('mudata.h5mu')
26
27 #else if $operation.mode == 'export'
28 mdata = mu.read_h5mu('$operation.mudata_in')
29 for mod in mdata.mod:
30 mdata[mod].write_h5ad(mod + '.h5ad')
31
32 #end if
33
34 ]]></configfile>
35 </configfiles>
36 <inputs>
37 <conditional name="operation">
38 <param name="mode" type="select" label="Mode of operation">
39 <option value="import" selected="true">Import multiple Anndata objects into a MuData object</option>
40 <option value="export">Export Anndata objects from a MuData objects</option>
41 </param>
42 <when value="import">
43 <repeat name="modalities" title="Modalities" min="2" default="2">
44 <param name="name" type="text" label="Modality name" value=""
45 help="Name to give for the modality in the MuData object">
46 <expand macro="sanitize_string" />
47 </param>
48 <param name="anndata" type="data" format="h5ad" label="Anndata object for the modality"/>
49 </repeat>
50 <param name="make_unique" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make variable names unique?"/>
51 </when>
52 <when value="export">
53 <param name="mudata_in" type="data" format="h5ad" label="Multimodal MuData object"/>
54 </when>
55 </conditional>
56 <expand macro="inputs_common_advanced" />
57 </inputs>
58 <outputs>
59 <data name="mudata_out" format="h5ad" from_work_dir="mudata.h5mu" label="MuData object built from ${on_string}">
60 <filter>operation['mode'] == 'import' </filter>
61 </data>
62 <collection name="collection_anndata" type="list" label="Anndata objects extracted from ${on_string}">
63 <discover_datasets pattern="(?P&lt;designation&gt;.*).h5ad" format="h5ad"/>
64 <filter>operation['mode'] == 'export' </filter>
65 </collection>
66 <expand macro="outputs_common_advanced"/>
67 </outputs>
68 <tests>
69 <test expect_num_outputs="2">
70 <!--Import test for RNA and ATAC modalities-->
71 <conditional name="operation">
72 <param name="mode" value="import"/>
73 <repeat name="modalities">
74 <param name="name" value="RNA"/>
75 <param name="anndata" location="https://zenodo.org/records/12570984/files/rna.h5ad"/>
76 </repeat>
77 <repeat name="modalities">
78 <param name="name" value="ATAC"/>
79 <param name="anndata" location="https://zenodo.org/records/12570984/files/atac.h5ad"/>
80 </repeat>
81 <param name="make_unique" value="True"/>
82 </conditional>
83 <section name="advanced_common">
84 <param name="show_log" value="true" />
85 </section>
86 <output name="hidden_output">
87 <assert_contents>
88 <has_text_matching expression="mu.MuData"/>
89 <has_text_matching expression="'RNA': ad.read"/>
90 <has_text_matching expression="'ATAC': ad.read"/>
91 <has_text_matching expression="var_names_make_unique()"/>
92 </assert_contents>
93 </output>
94 <output name="mudata_out" ftype="h5ad">
95 <assert_contents>
96 <has_h5_keys keys="mod/RNA"/>
97 <has_h5_keys keys="mod/ATAC"/>
98 <has_h5_keys keys="var/feature_types"/>
99 </assert_contents>
100 </output>
101 </test>
102 <test expect_num_outputs="2">
103 <!--Export test for RNA and ATAC modalities-->
104 <conditional name="operation">
105 <param name="mode" value="export"/>
106 <param name="mudata_in" location="https://zenodo.org/records/12570984/files/rna_atac.h5mu"/>
107 </conditional>
108 <section name="advanced_common">
109 <param name="show_log" value="true" />
110 </section>
111 <output name="hidden_output">
112 <assert_contents>
113 <has_text_matching expression="mu.read_h5mu"/>
114 <has_text_matching expression="write_h5ad"/>
115 </assert_contents>
116 </output>
117 <output_collection name="collection_anndata" type="list" count="2">
118 <element name="ATAC" ftype="h5ad">
119 <assert_contents>
120 <has_h5_keys keys="var/gene_ids"/>
121 <has_h5_keys keys="uns/neighbors"/>
122 <has_h5_keys keys="obsp/connectivities"/>
123 </assert_contents>
124 </element>
125 <element name="RNA" ftype="h5ad">
126 <assert_contents>
127 <has_h5_keys keys="var/gene_ids"/>
128 <has_h5_keys keys="uns/neighbors"/>
129 <has_h5_keys keys="obsp/connectivities"/>
130 </assert_contents>
131 </element>
132 </output_collection>
133 </test>
134 </tests>
135 <help><![CDATA[
136 **What it does**
137 Create MuData from AnnData is a tool that allows creating a muon.MuData object out of two or more AnnData objects
138 for multimodal analysis. The multimodal data is created by combining AnnData objects as
139 h5ad files into a MuData object as a h5mu file using muon.
140 Furthermore, it runs pp.intersect_obs to keep only entries present in both modalities (AnnData objects) in the
141 final MuData file.
142 ]]></help>
143 <expand macro="citations"/>
144 </tool>