Mercurial > repos > iuc > anndata_export

annotate export.xml @ 5:379014a57491 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
author iuc
date Wed, 05 Feb 2020 19:19:45 -0500
parents 8623710d083c
children 707023fa62fe
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1 <tool id="anndata_export" name="Export AnnData and loom files" version="@VERSION@+@GALAXY_VERSION@">
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2 <description>Interconvert AnnData and Loom formats</description>
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3 <macros>
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4 <import>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_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $hd5_format.filetype == 'anndata':
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10 @CMD@
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11 #else:
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12 @LOOMCMD@
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13 #end if
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14 ]]></command>
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15 <configfiles>
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16 <configfile name="script_file"><![CDATA[
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17 @CMD_imports@
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18 #if $hd5_format.filetype == 'anndata':
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19 adata = ad.read('$hd5_format.input')
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20 #if $hd5_format.output_format == 'loom':
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21 adata.write_loom('anndata.loom')
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22 #else if $hd5_format.output_format == 'tabular':
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23 adata.write_csvs('.', sep="\t", skip_data = False)
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24 #end if
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25 #end if
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26 ]]></configfile>
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27 </configfiles>
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28 <inputs>
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29 <conditional name="hd5_format">
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30 <param name="filetype" type="select" label="hd5 format">
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31 <option value="anndata" selected="true">Anndata file</option>
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32 <option value="loom">Loom file</option>
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33 </param>
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34 <when value="anndata">
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35 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
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36 <param name="output_format" type="select" label="Format to write the annotated data matrix">
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37 <option value="loom">loom</option>
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38 <option value="tabular">Tabular</option>
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39 </param>
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40 </when>
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41 <when value="loom">
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42 <param name="input" type="data" format="loom" label="Loom file to be exported to a series of tabular files."/>
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43 </when>
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44 </conditional>
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45 </inputs>
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46 <outputs>
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47 <data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
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48 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'loom'</filter>
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49 </data>
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50 <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)">
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51 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
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52 </data>
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53 <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)">
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54 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
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55 </data>
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56 <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)">
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57 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
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58 </data>
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59 <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)">
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60 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
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61 </data>
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62 <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)">
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63 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
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64 </data>
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65 <collection name="layer_tsvs" type="list" label="Layer matrices" >
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66 <filter>hd5_format['filetype'] == 'loom'</filter>
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67 <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
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68 </collection>
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69 <collection name="attribute_tsvs" type="list" label="Attribute matrices" >
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70 <filter>hd5_format['filetype'] == 'loom'</filter>
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71 <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
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72 </collection>
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73 </outputs>
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74 <tests>
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75 <test expect_num_outputs="1">
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76 <param name="filetype" value="anndata"/>
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77 <param name="input" value="krumsiek11.h5ad"/>
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78 <param name="output_format" value="loom"/>
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79 <assert_stdout>
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80 <has_text_matching expression="adata.write_loom"/>
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81 </assert_stdout>
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82 <output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
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83 </test>
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84 <test expect_num_outputs="5">
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85 <param name="filetype" value="anndata"/>
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86 <param name="input" value="krumsiek11.h5ad"/>
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87 <param name="output_format" value="tabular"/>
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88 <assert_stdout>
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89 <has_text_matching expression="adata.write_csvs"/>
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90 </assert_stdout>
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91 <output name="tabular_x" value="export.krumsiek11.X.tabular" ftype="tabular"/>
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92 <output name="tabular_obs" value="export.krumsiek11.obs.tabular" ftype="tabular"/>
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93 <output name="tabular_obsm" value="export.krumsiek11.obsm.tabular" ftype="tabular"/>
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94 <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
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95 <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
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96 </test>
3
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97 <test expect_num_outputs="2">
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98 <param name="filetype" value="loom"/>
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99 <param name="input" value="loomtest.loom"/>
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100 <output_collection name="layer_tsvs" type="list">
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101 <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
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102 <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
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103 <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
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104 </output_collection>
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105 <output_collection name="attribute_tsvs" type="list">
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106 <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
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107 <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
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108 </output_collection>
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109 </test>
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110 </tests>
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111 <help><![CDATA[
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112 This tool exports an AnnData dataset to a Loom file
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113 (`write_loom method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_loom.html>`__)
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114 or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_csvs.html>`__)
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115
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116 It can also create a series of tabular files from an input loom dataset.
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117
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118 @HELP@
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119 ]]></help>
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120 <expand macro="citations"/>
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121 </tool>