Mercurial > repos > iuc > anndata_manipulate
changeset 2:a56baceb1900 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
| author | iuc |
|---|---|
| date | Thu, 12 Dec 2019 09:22:35 -0500 |
| parents | 19592ec717ef |
| children | 6db1b06e6bbb |
| files | macros.xml manipulate.xml test-data/manipulate.save_raw.h5ad |
| diffstat | 3 files changed, 17 insertions(+), 2 deletions(-) [+] |
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--- a/macros.xml Wed Oct 16 06:26:45 2019 -0400 +++ b/macros.xml Thu Dec 12 09:22:35 2019 -0500 @@ -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>
--- a/manipulate.xml Wed Oct 16 06:26:45 2019 -0400 +++ b/manipulate.xml Thu Dec 12 09:22:35 2019 -0500 @@ -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"/>