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Update Anndata to 0.10.9 #6309

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Sep 14, 2024
Merged

Update Anndata to 0.10.9 #6309

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fc03c16
Update Anndata to 0.10.9
pavanvidem Sep 6, 2024
4de98de
replace h5ad size comparison with h5 asserts
pavanvidem Sep 9, 2024
e0a651c
fix linting and remove h5ad test data
pavanvidem Sep 9, 2024
0bf651c
add tests for newly added functions
pavanvidem Sep 10, 2024
9a531cc
add gzip compression for all h5ad files
pavanvidem Sep 10, 2024
0343a4c
add help text about newly added functions and update tests
pavanvidem Sep 11, 2024
bd992d4
fix tests
pavanvidem Sep 11, 2024
fe812e7
remove flagged.h5ad
pavanvidem Sep 11, 2024
011951c
move all loompy functions to modify_loom
pavanvidem Sep 11, 2024
53470b2
trying to fix tests
pavanvidem Sep 12, 2024
48b01d4
fix anndata to loom
pavanvidem Sep 12, 2024
30a636f
fix
pavanvidem Sep 12, 2024
959a8d1
move all loom functions to modify_loom.xml and fix tests
pavanvidem Sep 13, 2024
4196c66
change output loom name to fix the test
pavanvidem Sep 14, 2024
320fb61
re-add all the tests to modify_loom
pavanvidem Sep 14, 2024
0b4f26b
review suggestions
pavanvidem Sep 14, 2024
953f226
fix the order of elements in collection
pavanvidem Sep 14, 2024
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96 changes: 11 additions & 85 deletions tools/anndata/export.xml
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Original file line number Diff line number Diff line change
@@ -1,90 +1,33 @@
<tool id="anndata_export" name="Export AnnData and loom files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<description>Interconvert AnnData and Loom formats</description>
<tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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please add, make sure, a profile version is in all tools

Suggested change
<tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">

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set profile to 21.09 (same as scanpy) to support other instances. See here: #6001

<description>matrix and annotations</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="exit_code"><![CDATA[
#if $hd5_format.filetype == 'anndata':
@CMD@
#else:
@LOOMCMD@
#end if
@CMD@
]]></command>
<configfiles>
<configfile name="script_file"><![CDATA[
@CMD_imports@
#if $hd5_format.filetype == 'anndata':
adata = ad.read_h5ad('$hd5_format.input')
#if $hd5_format.output_format == 'loom':
adata.write_loom('anndata.loom')
#else if $hd5_format.output_format == 'tabular':
adata = ad.read_h5ad('$input')
adata.write_csvs('.', sep="\t", skip_data = False)
#end if
#end if
]]></configfile>
</configfiles>
<inputs>
<conditional name="hd5_format">
<param name="filetype" type="select" label="hd5 format">
<option value="anndata" selected="true">Anndata file</option>
<option value="loom">Loom file</option>
</param>
<when value="anndata">
<param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
<param name="output_format" type="select" label="Format to write the annotated data matrix">
<option value="loom">loom</option>
<option value="tabular">Tabular</option>
</param>
</when>
<when value="loom">
<param name="input" type="data" format="loom" label="Loom file to be exported to a series of tabular files."/>
</when>
</conditional>
<param name="input" type="data" format="h5ad" label="Annotated data matrix to export" help="Create individual tabular files for matrix, obs, obsm, var and varm annotations"/>
</inputs>
<outputs>
<data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
<filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'loom'</filter>
</data>
<data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)">
<filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
</data>
<data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)">
<filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
</data>
<data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)">
<filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
</data>
<data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)">
<filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
</data>
<data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)">
<filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
</data>
<collection name="layer_tsvs" type="list" label="Layer matrices" >
<filter>hd5_format['filetype'] == 'loom'</filter>
<discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
</collection>
<collection name="attribute_tsvs" type="list" label="Attribute matrices" >
<filter>hd5_format['filetype'] == 'loom'</filter>
<discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
</collection>
<data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"/>
<data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)"/>
<data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)"/>
<data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)"/>
<data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)"/>
</outputs>
<tests>
<test expect_num_outputs="1">
<param name="filetype" value="anndata"/>
<param name="input" value="krumsiek11.h5ad"/>
<param name="output_format" value="loom"/>
<assert_stdout>
<has_text_matching expression="adata.write_loom"/>
</assert_stdout>
<output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
</test>
<test expect_num_outputs="5">
<param name="filetype" value="anndata"/>
<param name="input" value="krumsiek11.h5ad"/>
<param name="output_format" value="tabular"/>
<assert_stdout>
<has_text_matching expression="adata.write_csvs"/>
</assert_stdout>
Expand All @@ -94,26 +37,9 @@ adata.write_csvs('.', sep="\t", skip_data = False)
<output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
<output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
</test>
<test expect_num_outputs="2">
<param name="filetype" value="loom"/>
<param name="input" value="loomtest.loom"/>
<output_collection name="layer_tsvs" type="list">
<element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
<element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
<element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
</output_collection>
<output_collection name="attribute_tsvs" type="list">
<element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
<element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
</output_collection>
</test>
</tests>
<help><![CDATA[
This tool exports an AnnData dataset to a Loom file
(`write_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_loom.html>`__)
or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)

It can also create a series of tabular files from an input loom dataset.
This tool exports an AnnData dataset to a tabular files (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)

@HELP@
]]></help>
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