| Previous changeset 1:19592ec717ef (2019-10-16) Next changeset 3:6db1b06e6bbb (2020-01-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" |
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modified:
macros.xml manipulate.xml |
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added:
test-data/manipulate.save_raw.h5ad |
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| diff -r 19592ec717ef -r a56baceb1900 macros.xml --- a/macros.xml Wed Oct 16 06:26:45 2019 -0400 +++ b/macros.xml Thu Dec 12 09:22:35 2019 -0500 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@VERSION@">0.6.22.post1</token> - <token name="@GALAXY_VERSION@">galaxy0</token> + <token name="@GALAXY_VERSION@">galaxy1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">anndata</requirement> |
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| diff -r 19592ec717ef -r a56baceb1900 manipulate.xml --- a/manipulate.xml Wed Oct 16 06:26:45 2019 -0400 +++ b/manipulate.xml Thu Dec 12 09:22:35 2019 -0500 |
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| @@ -120,6 +120,10 @@ #else if $manipulate.var_obs == 'obs' adata = adata[filtered, :] #end if + +#else if $manipulate.function == 'save_raw' +adata.raw = adata + #end if adata.write('anndata.h5ad') @@ -137,6 +141,7 @@ <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option> <option value="add_annotation">Add new annotation(s) for observations or variables</option> <option value="filter">Filter observations or variables</option> + <option value="save_raw">Freeze the current state into the 'raw' attribute</option> </param> <when value="concatenate"> <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/> @@ -173,7 +178,7 @@ help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/> </when> <when value="filter"> - <param name="var_obs" type="select" label="What to annotate?"> + <param name="var_obs" type="select" label="What to filter?"> <option value="var">Variables (var)</option> <option value="obs">Observations (obs)</option> </param> @@ -368,6 +373,14 @@ </conditional> <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/> </test> + <test> + <!-- test 11 --> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="save_raw"/> + </conditional> + <output name="anndata" value="manipulate.save_raw.h5ad" ftype="h5ad" compare="sim_size"/> + </test> </tests> <help><![CDATA[ **What it does** @@ -406,6 +419,8 @@ - Filter data variables or observations, by index or key +- Freeze the current state into the 'raw' attribute + @HELP@ ]]></help> <expand macro="citations"/> |
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| diff -r 19592ec717ef -r a56baceb1900 test-data/manipulate.save_raw.h5ad |
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| Binary file test-data/manipulate.save_raw.h5ad has changed |