Mercurial > repos > iuc > anndata_export

annotate export.xml @ 0:fcb7370e827f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
author iuc
date Wed, 10 Apr 2019 03:24:14 -0400
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children 8623710d083c
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fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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1 <tool id="anndata_export" name="Export AnnData" version="@VERSION@+@GALAXY_VERSION@">
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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2 <description>to different formats</description>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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3 <macros>
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4 <import>macros.xml</import>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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5 </macros>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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6 <expand macro="requirements"/>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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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
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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15 adata = ad.read('$input')
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16 #if $output_format == 'loom'
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17 adata.write_loom('anndata.loom')
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18 #else if $output_format == 'tabular'
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19 adata.write_csvs('.', sep="\t", skip_data = False)
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20 #end if
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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21 ]]></configfile>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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22 </configfiles>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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23 <inputs>
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24 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
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25 <param name="output_format" type="select" label="Format to write the annotated data matrix">
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26 <option value="loom">loom</option>
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27 <option value="tabular">Tabular</option>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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28 </param>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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29 </inputs>
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30 <outputs>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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31 <data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
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32 <filter>output_format == 'loom'</filter>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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33 </data>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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34 <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)">
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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35 <filter>output_format == 'tabular'</filter>
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36 </data>
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37 <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)">
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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38 <filter>output_format == 'tabular'</filter>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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39 </data>
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40 <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)">
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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41 <filter>output_format == 'tabular'</filter>
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42 </data>
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43 <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)">
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44 <filter>output_format == 'tabular'</filter>
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45 </data>
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46 <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)">
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47 <filter>output_format == 'tabular'</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input" value="krumsiek11.h5ad"/>
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53 <param name="output_format" value="loom"/>
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54 <assert_stdout>
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55 <has_text_matching expression="adata.write_loom"/>
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56 </assert_stdout>
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57 <output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
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58 </test>
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59 <test>
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60 <param name="input" value="krumsiek11.h5ad"/>
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61 <param name="output_format" value="tabular"/>
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62 <assert_stdout>
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63 <has_text_matching expression="adata.write_csvs"/>
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64 </assert_stdout>
fcb7370e827f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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65 <output name="tabular_x" value="export.krumsiek11.X.tabular" ftype="tabular"/>
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66 <output name="tabular_obs" value="export.krumsiek11.obs.tabular" ftype="tabular"/>
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67 <output name="tabular_obsm" value="export.krumsiek11.obsm.tabular" ftype="tabular"/>
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68 <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
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69 <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 **What it does**
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74
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75 This tool exports a AnnData dataset to a Loom file
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76 (`write_loom method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_loom.html>`__)
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77 or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_csvs.html>`__)
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78
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79 @HELP@
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80 ]]></help>
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81 <expand macro="citations"/>
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82 </tool>