Mercurial > repos > iuc > anndata_manipulate
diff manipulate.xml @ 12:ed4996a16f7f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
author | iuc |
---|---|
date | Sun, 12 Nov 2023 16:42:25 +0000 |
parents | 3d748954434b |
children | 7e8c677a7b71 |
line wrap: on
line diff
--- a/manipulate.xml Wed Jun 22 07:21:03 2022 +0000 +++ b/manipulate.xml Sun Nov 12 16:42:25 2023 +0000 @@ -20,11 +20,11 @@ <configfile name="script_file"><![CDATA[ @CMD_imports@ -adata = ad.read('$input') +adata = ad.read_h5ad('$input') #if $manipulate.function == 'concatenate' #for i, filepath in enumerate($manipulate.other_adatas) -adata_$i = ad.read('$filepath') +adata_$i = ad.read_h5ad('$filepath') #end for adata = adata.concatenate( #for i, filepath in enumerate($manipulate.other_adatas) @@ -174,7 +174,7 @@ <option value="var">Variables (var)</option> <option value="obs">Observations (obs)</option> </param> - <param name="new_annot" type="data" format="tabular" label="Table with new annotations" + <param name="new_annot" type="data" format="tabular" label="Table with new annotations" 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"> @@ -289,12 +289,12 @@ <conditional name="manipulate"> <param name="function" value="rename_categories"/> <param name="key" value="cell_type"/> - <param name="categories" value="Er,Ml,Mt, Ne, pr"/> + <param name="categories" value="Ery, Mk, Mo, progenitor"/> </conditional> <assert_stdout> <has_text_matching expression="adata.rename_categories"/> <has_text_matching expression="key='cell_type'"/> - <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/> + <has_text_matching expression="categories=\['Ery', 'Mk', 'Mo', 'progenitor'\]"/> </assert_stdout> <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/> </test>