diff macros.xml @ 3:286a24ac079c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"

--- a/macros.xml	Thu Dec 12 09:23:54 2019 -0500
+++ b/macros.xml	Mon Jan 06 13:45:39 2020 -0500
@@ -15,13 +15,19 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command><![CDATA[python -c "import anndata as ad;print('anndata version: %s' % ad.__version__)"]]></version_command>
+        <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>
     </xml>
     <token name="@CMD@"><![CDATA[
 cat '$script_file' &&
 python '$script_file'
     ]]>
     </token>
+    <token name="@LOOMCMD@"><![CDATA[
+mkdir ./output &&
+mkdir ./attributes &&
+python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}'
+    ]]>
+    </token>
     <token name="@CMD_imports@"><![CDATA[
 import anndata as ad
     ]]>
@@ -33,15 +39,27 @@
 
 AnnData stores a data matrix `X` together with annotations of observations `obs`, variables `var` and unstructured annotations `uns`.
 
-.. image:: https://falexwolf.de/img/scanpy/anndata.svg 
+.. image:: https://falexwolf.de/img/scanpy/anndata.svg
 
 
-AnnData stores observations (samples) of variables (features) in the rows of a matrix. This is the convention of the modern classics 
-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 
+AnnData stores observations (samples) of variables (features) in the rows of a matrix. This is the convention of the modern classics
+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
 and machine learning packages in Python (statsmodels, scikit-learn).
 
 More details on the `AnnData documentation
 <https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__
+
+
+**Loom data**
+
+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.
+
+.. image:: https://linnarssonlab.org/loompy/_images/Loom_components.png
+
+
+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
+and cells, such as Name, Chromosome, Position (for genes), and Strain, Sex, Age (for cells).
+
     ]]>
     </token>
     <xml name="params_chunk_X">