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comparison macros.xml @ 3:8623710d083c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
author iuc
date Mon, 06 Jan 2020 13:44:46 -0500
parents e0395cca2c57
children 016308443041
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2:e0395cca2c57 3:8623710d083c
13 <citations> 13 <citations>
14 <citation type="doi">10.1186/s13059-017-1382-0</citation> 14 <citation type="doi">10.1186/s13059-017-1382-0</citation>
15 </citations> 15 </citations>
16 </xml> 16 </xml>
17 <xml name="version_command"> 17 <xml name="version_command">
18 <version_command><![CDATA[python -c "import anndata as ad;print('anndata version: %s' % ad.__version__)"]]></version_command> 18 <version_command><![CDATA[python -c "import anndata as ad;print('anndata version: %s' % ad.__version__); import loompy;print('\nloompy version: %s' % loompy.__version__)"]]></version_command>
19 </xml> 19 </xml>
20 <token name="@CMD@"><![CDATA[ 20 <token name="@CMD@"><![CDATA[
21 cat '$script_file' && 21 cat '$script_file' &&
22 python '$script_file' 22 python '$script_file'
23 ]]>
24 </token>
25 <token name="@LOOMCMD@"><![CDATA[
26 mkdir ./output &&
27 mkdir ./attributes &&
28 python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}'
23 ]]> 29 ]]>
24 </token> 30 </token>
25 <token name="@CMD_imports@"><![CDATA[ 31 <token name="@CMD_imports@"><![CDATA[
26 import anndata as ad 32 import anndata as ad
27 ]]> 33 ]]>
31 37
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. 38 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 39
34 AnnData stores a data matrix `X` together with annotations of observations `obs`, variables `var` and unstructured annotations `uns`. 40 AnnData stores a data matrix `X` together with annotations of observations `obs`, variables `var` and unstructured annotations `uns`.
35 41
36 .. image:: https://falexwolf.de/img/scanpy/anndata.svg 42 .. image:: https://falexwolf.de/img/scanpy/anndata.svg
37 43
38 44
39 AnnData stores observations (samples) of variables (features) in the rows of a matrix. This is the convention of the modern classics 45 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 46 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). 47 and machine learning packages in Python (statsmodels, scikit-learn).
42 48
43 More details on the `AnnData documentation 49 More details on the `AnnData documentation
44 <https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__ 50 <https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__
51
52
53 **Loom data**
54
55 Loom files are an efficient file format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations, and sparse graph objects.
56
57 .. image:: https://linnarssonlab.org/loompy/_images/Loom_components.png
58
59
60 Loom files to store single-cell gene expression data: the main matrix contains the actual expression values (one column per cell, one row per gene); row and column annotations contain metadata for genes
61 and cells, such as Name, Chromosome, Position (for genes), and Strain, Sex, Age (for cells).
62
45 ]]> 63 ]]>
46 </token> 64 </token>
47 <xml name="params_chunk_X"> 65 <xml name="params_chunk_X">
48 <conditional name="chunk"> 66 <conditional name="chunk">
49 <param name="info" type="select" label="How to select the chunk?"> 67 <param name="info" type="select" label="How to select the chunk?">