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comparison macros.xml @ 0:0ef28c0963c8 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 03:25:05 -0400
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children 19592ec717ef
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-1:000000000000 0:0ef28c0963c8
1 <macros>
2 <token name="@VERSION@">0.6.19</token>
3 <token name="@GALAXY_VERSION@">galaxy0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@VERSION@">anndata</requirement>
7 <requirement type="package" version="1.4">scanpy</requirement>
8 <requirement type="package" version="2.0.17">loompy</requirement>
9 <yield />
10 </requirements>
11 </xml>
12 <xml name="citations">
13 <citations>
14 <citation type="doi">10.1186/s13059-017-1382-0</citation>
15 </citations>
16 </xml>
17 <xml name="version_command">
18 <version_command><![CDATA[python -c "import anndata as ad;print('anndata version: %s' % ad.__version__)"]]></version_command>
19 </xml>
20 <token name="@CMD@"><![CDATA[
21 cat '$script_file' &&
22 python '$script_file'
23 ]]>
24 </token>
25 <token name="@CMD_imports@"><![CDATA[
26 import anndata as ad
27 ]]>
28 </token>
29 <token name="@HELP@"><![CDATA[
30 **AnnData**
31
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.
33
34 AnnData stores a data matrix `X` together with annotations of observations `obs`, variables `var` and unstructured annotations `uns`.
35
36 .. image:: https://falexwolf.de/img/scanpy/anndata.svg
37
38
39 AnnData stores observations (samples) of variables (features) in the rows of a matrix. This is the convention of the modern classics
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
41 and machine learning packages in Python (statsmodels, scikit-learn).
42
43 More details on the `AnnData documentation
44 <https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__
45 ]]>
46 </token>
47 <xml name="params_chunk_X">
48 <conditional name="chunk">
49 <param name="info" type="select" label="How to select the chunk?">
50 <option value="random">Random chunk of defined size</option>
51 <option value="specified">Specified indices</option>
52 </param>
53 <when value="random">
54 <param name="size" type="integer" value="1000" label="Size of chunk to randomly select"/>
55 <param name="replace" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Random sampling of indices with replacement?"/>
56 </when>
57 <when value="specified">
58 <param name="list" type="text" value="" label="List of comma-separated indices to return"/>
59 </when>
60 </conditional>
61 </xml>
62 </macros>