Mercurial > repos > iuc > anndata2ri

annotate anndata2ri.xml @ 0:ac675f28acfc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata2ri/ commit f2b398613762cdee5f89fb43382df2bf7321ccde
author iuc
date Thu, 13 Feb 2025 10:38:32 +0000
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ac675f28acfc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata2ri/ commit f2b398613762cdee5f89fb43382df2bf7321ccde
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1 <tool id="anndata2ri" name="anndata2ri" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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2 <description>
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3 Convert between Anndata and SingCellExperiment objects
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4 </description>
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5 <macros>
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6 <token name="@TOOL_VERSION@">1.3.2</token>
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7 <token name="@VERSION_SUFFIX@">0</token>
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8 </macros>
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9 <xrefs>
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10 <xref type="bio.tools">anndata2ri</xref>
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11 </xrefs>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">anndata2ri</requirement>
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14 <requirement type="package" version="0.10.9">anndata</requirement>
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15 <requirement type="package" version="1.24.0">bioconductor-singlecellexperiment</requirement>
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16 </requirements>
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17 <command detect_errors="exit_code"><![CDATA[
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18 python '$script_file' '$conversion.direction'
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19 ]]></command>
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20 <configfiles>
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21 <configfile name="script_file"><![CDATA[
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22 import sys
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23 import anndata as ad
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24 import anndata2ri
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25 import rpy2.robjects as ro
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26 from rpy2.rlike.container import OrdDict
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27
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28 ro.r('suppressPackageStartupMessages(library(SingleCellExperiment))')
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29
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30 def convert_orddict_to_dict(uns):
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31 if isinstance(uns, OrdDict):
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32 return {k: convert_orddict_to_dict(v) for k, v in uns.items()}
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33 elif isinstance(uns, list):
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34 return [convert_orddict_to_dict(v) for v in uns]
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35 elif isinstance(uns, tuple):
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36 return tuple(convert_orddict_to_dict(v) for v in uns)
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37 elif isinstance(uns, dict):
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38 return {k: convert_orddict_to_dict(v) for k, v in uns.items()}
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39 else:
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40 return uns
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41
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42 if sys.argv[1] == 'sce2anndata':
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43 sce = ro.r('readRDS')('$conversion.input_object')
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44 with ro.conversion.localconverter(ro.default_converter + anndata2ri.converter):
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45 adata = ro.conversion.rpy2py(sce)
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46 adata.uns = convert_orddict_to_dict(adata.uns)
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47 adata.obs.index = adata.obs.index.astype(str)
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48 adata.var.index = adata.var.index.astype(str)
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49 adata.write('outfile.h5ad', compression='gzip')
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50
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51 elif sys.argv[1] == 'anndata2sce':
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52 adata = ad.read_h5ad('$conversion.input_object')
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53 with ro.conversion.localconverter(ro.default_converter + anndata2ri.converter):
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54 sce = ro.conversion.py2rpy(adata)
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55 ro.r('saveRDS')(sce, 'outfile.rds')
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56
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57 ]]></configfile>
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58 </configfiles>
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59 <inputs>
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60 <conditional name="conversion" >
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61 <param name="direction" type="select" label="Convert From / To" >
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62 <option value="sce2anndata" >SingleCellexperiment to AnnData</option>
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63 <option value="anndata2sce" >AnnData to SingleCellexperiment</option>
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64 </param>
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65 <when value="sce2anndata">
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66 <param name="input_object" type="data" format="rdata.sce,rds" label="SingCellExperiment object to convert" />
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67 </when>
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68 <when value="anndata2sce" >
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69 <param name="input_object" type="data" format="h5ad,h5" label="Anndata object to convert"/>
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70 </when>
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71 </conditional>
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72 </inputs>
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73 <outputs>
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74 <data name="output_anndata" format="h5ad" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: Anndata object">
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75 <filter>conversion['direction'] == 'sce2anndata'</filter>
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76 </data>
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77 <data name="output_sce" format="rdata.sce" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: SingleCellExperiment object">
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78 <filter>conversion['direction'] == 'anndata2sce'</filter>
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79 </data>
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80 </outputs>
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81 <tests>
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82 <test expect_num_outputs="1">
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83 <param name="direction" value="sce2anndata"/>
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84 <param name="input_object" value="krumsiek11.rds"/>
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85 <output name="output_anndata" file="krumsiek11.h5ad" ftype="h5ad" compare="sim_size">
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86 <assert_contents>
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87 <has_h5_keys keys="obs/cell_type"/>
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88 <has_h5_keys keys="uns/highlights"/>
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89 <has_h5_keys keys="uns/iroot"/>
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90 </assert_contents>
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91 </output>
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92 </test>
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93 <test expect_num_outputs="1">
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94 <param name="direction" value="anndata2sce"/>
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95 <param name="input_object" value="krumsiek11.h5ad"/>
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96 <output name="output_sce" file="krumsiek11.rds" ftype="rdata.sce" compare="sim_size"/>
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100 anndata2ri
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101 ==========
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102 Convert between Anndata and SingleCellExperiment objects. For conversion of further single-cell file formats, consider using **SCEasy Converter** tool.
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103 ]]></help>
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104 <citations>
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105 <citation type="bibtex">
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106 @unpublished{anndata2ri,
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107 author = {Theis Lab},
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108 title = {Convert between AnnData and SingleCellExperiment },
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109 url = {https://github.com/theislab/anndata2ri}
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110 }
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111 </citation>
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112 </citations>
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113 </tool>