Mercurial > repos > iuc > anndata_export

annotate export.xml @ 15:482689186cb8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5
author iuc
date Wed, 10 Dec 2025 16:58:55 +0000
parents 155982133d99
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1 <tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>matrix and annotations</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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @CMD@
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="script_file"><![CDATA[
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14 @CMD_imports@
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15 adata = ad.read_h5ad('$input')
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16 adata.write_csvs('.', sep="\t", skip_data = False)
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17 ]]></configfile>
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18 </configfiles>
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19 <inputs>
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20 <param name="input" type="data" format="h5ad" label="Annotated data matrix to export" help="Create individual tabular files for matrix, obs, obsm, var and varm annotations"/>
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21 </inputs>
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22 <outputs>
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23 <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"/>
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24 <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)"/>
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25 <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)"/>
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26 <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)"/>
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27 <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)"/>
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28 </outputs>
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29 <tests>
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30 <test expect_num_outputs="5">
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31 <param name="input" value="krumsiek11.h5ad"/>
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32 <assert_stdout>
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33 <has_text_matching expression="adata.write_csvs"/>
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34 </assert_stdout>
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35 <output name="tabular_x" value="export.krumsiek11.X.tabular" ftype="tabular"/>
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36 <output name="tabular_obs" value="export.krumsiek11.obs.tabular" ftype="tabular"/>
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37 <output name="tabular_obsm" value="export.krumsiek11.obsm.tabular" ftype="tabular"/>
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38 <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
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39 <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 This tool exports an AnnData dataset to a tabular files (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)
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45 @HELP@
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46 ]]></help>
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47 <expand macro="citations"/>
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48 </tool>