Mercurial > repos > iuc > anndata_manipulate

annotate macros.xml @ 7:43cb7b5a6fe7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
author iuc
date Wed, 22 Jul 2020 12:21:13 -0400
parents b03c60f8528f
children b85871dd69f9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
1 <macros>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2 <token name="@VERSION@">0.6.22.post1</token>
7
43cb7b5a6fe7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
iuc
parents: 5
diff changeset
3 <token name="@GALAXY_VERSION@">galaxy4</token>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
4 <xml name="requirements">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
5 <requirements>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
6 <requirement type="package" version="@VERSION@">anndata</requirement>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
7 <requirement type="package" version="2.0.17">loompy</requirement>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
8 <requirement type="package" version="2.9.0">h5py</requirement>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
9 <yield />
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
10 </requirements>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
11 </xml>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
12 <xml name="citations">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
13 <citations>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
15 </citations>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
16 </xml>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
17 <xml name="version_command">
3
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
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>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
19 </xml>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
20 <token name="@CMD@"><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
21 cat '$script_file' &&
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
22 python '$script_file'
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
23 ]]>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
24 </token>
3
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
25 <token name="@LOOMCMD@"><![CDATA[
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
26 mkdir ./output &&
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
27 mkdir ./attributes &&
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
28 python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}'
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
29 ]]>
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
30 </token>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
31 <token name="@CMD_imports@"><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
32 import anndata as ad
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
33 ]]>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
34 </token>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
35 <token name="@HELP@"><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
36 **AnnData**
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
37
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
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.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
39
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
40 AnnData stores a data matrix `X` together with annotations of observations `obs`, variables `var` and unstructured annotations `uns`.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
41
3
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
42 .. image:: https://falexwolf.de/img/scanpy/anndata.svg
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
43
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
44
3
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
45 AnnData stores observations (samples) of variables (features) in the rows of a matrix. This is the convention of the modern classics
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
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
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
47 and machine learning packages in Python (statsmodels, scikit-learn).
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
48
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
49 More details on the `AnnData documentation
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
50 <https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__
3
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
51
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
52
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
53 **Loom data**
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
54
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
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.
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
56
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
57 .. image:: https://linnarssonlab.org/loompy/_images/Loom_components.png
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
58
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
59
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
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
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
61 and cells, such as Name, Chromosome, Position (for genes), and Strain, Sex, Age (for cells).
6db1b06e6bbb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
62
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
63 ]]>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
64 </token>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
65 <xml name="params_chunk_X">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
66 <conditional name="chunk">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
67 <param name="info" type="select" label="How to select the chunk?">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
68 <option value="random">Random chunk of defined size</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
69 <option value="specified">Specified indices</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
70 </param>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
71 <when value="random">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
72 <param name="size" type="integer" value="1000" label="Size of chunk to randomly select"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
73 <param name="replace" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Random sampling of indices with replacement?"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
74 </when>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
75 <when value="specified">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
76 <param name="list" type="text" value="" label="List of comma-separated indices to return"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
77 </when>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
78 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
79 </xml>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
80 </macros>