Mercurial > repos > iuc > anndata_manipulate

annotate macros.xml @ 1:19592ec717ef draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author iuc
date Wed, 16 Oct 2019 06:26:45 -0400
parents 0ef28c0963c8
children a56baceb1900
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0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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1 <macros>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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2 <token name="@VERSION@">0.6.22.post1</token>
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3 <token name="@GALAXY_VERSION@">galaxy0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">anndata</requirement>
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7 <requirement type="package" version="2.0.17">loompy</requirement>
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19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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8 <requirement type="package" version="2.9.0">h5py</requirement>
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0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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9 <yield />
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10 </requirements>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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11 </xml>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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12 <xml name="citations">
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13 <citations>
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14 <citation type="doi">10.1186/s13059-017-1382-0</citation>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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15 </citations>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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16 </xml>
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17 <xml name="version_command">
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18 <version_command><![CDATA[python -c "import anndata as ad;print('anndata version: %s' % ad.__version__)"]]></version_command>
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19 </xml>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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20 <token name="@CMD@"><![CDATA[
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21 cat '$script_file' &&
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22 python '$script_file'
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23 ]]>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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24 </token>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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25 <token name="@CMD_imports@"><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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26 import anndata as ad
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27 ]]>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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28 </token>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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29 <token name="@HELP@"><![CDATA[
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30 **AnnData**
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31
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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32 AnnData provides a scalable way of keeping track of data together with learned annotations. It is used within `Scanpy <https://github.com/theislab/scanpy>`__, for which it was initially developed.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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33
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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34 AnnData stores a data matrix `X` together with annotations of observations `obs`, variables `var` and unstructured annotations `uns`.
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35
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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36 .. image:: https://falexwolf.de/img/scanpy/anndata.svg
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0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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39 AnnData stores observations (samples) of variables (features) in the rows of a matrix. This is the convention of the modern classics
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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40 of statistics (`Hastie et al., 2009 <https://web.stanford.edu/~hastie/ElemStatLearn/>`__) and machine learning (Murphy, 2012), the convention of dataframes both in R and Python and the established statistics
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41 and machine learning packages in Python (statsmodels, scikit-learn).
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43 More details on the `AnnData documentation
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44 <https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__
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45 ]]>
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46 </token>
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47 <xml name="params_chunk_X">
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48 <conditional name="chunk">
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49 <param name="info" type="select" label="How to select the chunk?">
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50 <option value="random">Random chunk of defined size</option>
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51 <option value="specified">Specified indices</option>
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52 </param>
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53 <when value="random">
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54 <param name="size" type="integer" value="1000" label="Size of chunk to randomly select"/>
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55 <param name="replace" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Random sampling of indices with replacement?"/>
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56 </when>
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57 <when value="specified">
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58 <param name="list" type="text" value="" label="List of comma-separated indices to return"/>
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59 </when>
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60 </conditional>
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61 </xml>
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62 </macros>