Mercurial > repos > iuc > scanpy_filter
diff filter.xml @ 11:2d02d9702d3a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
| author | iuc |
|---|---|
| date | Wed, 08 Nov 2023 14:44:39 +0000 |
| parents | b409c2486353 |
| children | a03ff8633507 |
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--- a/filter.xml Wed Sep 22 21:11:51 2021 +0000 +++ b/filter.xml Wed Nov 08 14:44:39 2023 +0000 @@ -1,9 +1,9 @@ <tool id="scanpy_filter" name="Filter" version="@galaxy_version@" profile="@profile@"> <description>with scanpy</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ @@ -52,7 +52,6 @@ groupby='$method.groupby', #end if use_raw=$method.use_raw, - log=$method.log, key_added='$method.key_added', min_in_group_fraction=$method.min_in_group_fraction, max_out_group_fraction=$method.max_out_group_fraction, @@ -173,7 +172,6 @@ <expand macro="sanitize_query" /> </param> <expand macro="param_use_raw"/> - <expand macro="param_log"/> <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values"> <expand macro="sanitize_query" /> </param> @@ -228,8 +226,8 @@ <expand macro="anndata_outputs"/> </outputs> <tests> - <test> - <!-- test 0 --> + <test expect_num_outputs="2"> + <!-- test 1 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.filter_cells"/> @@ -252,8 +250,8 @@ </output> <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 1 --> + <test expect_num_outputs="2"> + <!-- test 2 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.filter_cells"/> @@ -274,8 +272,8 @@ </output> <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 2 --> + <test expect_num_outputs="2"> + <!-- test 3 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.filter_genes"/> @@ -295,36 +293,41 @@ </output> <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <!-- <test> --> - <!-- <!-\- test 3 -\-> --> - <!-- <!-\- Input dataset appears to be missing rank_genes_groups key... -\-> --> - <!-- <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> --> - <!-- <conditional name="method"> --> - <!-- <param name="method" value="tl.filter_rank_genes_groups"/> --> - <!-- <param name="key" value="rank_genes_groups"/> --> - <!-- <param name="use_raw" value="False"/> --> - <!-- <param name="log" value="False"/> --> - <!-- <param name="key_added" value="rank_genes_groups_filtered"/> --> - <!-- <param name="min_in_group_fraction" value="0.25"/> --> - <!-- <param name="max_out_group_fraction" value="0.5"/> --> - <!-- <param name="min_fold_change" value="3"/> --> - <!-- </conditional> --> - <!-- <output name="hidden_output"> --> - <!-- <assert_contents> --> - <!-- <has_text_matching expression="tl.filter_rank_genes_groups"/> --> - <!-- <has_text_matching expression="key='rank_genes_groups'"/> --> - <!-- <has_text_matching expression="use_raw=False"/> --> - <!-- <has_text_matching expression="log=False"/> --> - <!-- <has_text_matching expression="key_added='rank_genes_groups_filtered'"/> --> - <!-- <has_text_matching expression="min_in_group_fraction=0.25"/> --> - <!-- <has_text_matching expression="max_out_group_fraction=0.5"/> --> - <!-- <has_text_matching expression="min_fold_change=3"/> --> - <!-- </assert_contents> --> - <!-- </output> --> - <!-- <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/> --> - <!-- </test> --> - <test> - <!-- test 4 --> + + <!-- test 4 --> + <!-- Fails to write to anndata after tl.filter_rank_genes_groups + Issue has been reported here: https://github.com/scverse/anndata/issues/726 + The current fix is: del adata.uns['rank_genes_groups_filtered'] --> + <!--<test expect_num_outputs="2"> + <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> + <conditional name="method"> + <param name="method" value="tl.filter_rank_genes_groups"/> + <param name="key" value="rank_genes_groups"/> + <param name="use_raw" value="False"/> + <param name="key_added" value="rank_genes_groups_filtered"/> + <param name="min_in_group_fraction" value="0.25"/> + <param name="max_out_group_fraction" value="0.5"/> + <param name="min_fold_change" value="3"/> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="tl.filter_rank_genes_groups"/> + <has_text_matching expression="key='rank_genes_groups'"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="log=False"/> + <has_text_matching expression="key_added='rank_genes_groups_filtered'"/> + <has_text_matching expression="min_in_group_fraction=0.25"/> + <has_text_matching expression="max_out_group_fraction=0.5"/> + <has_text_matching expression="min_fold_change=3"/> + </assert_contents> + </output> + <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/> + </test>--> + <test expect_num_outputs="2"> + <!-- test 5 --> <param name="adata" value="blobs.h5ad"/> <conditional name="method"> <param name="method" value="pp.highly_variable_genes"/> @@ -353,8 +356,8 @@ </output> <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.2"/> </test> - <test> - <!-- test 5 --> + <test expect_num_outputs="2"> + <!-- test 6 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.highly_variable_genes"/> @@ -379,8 +382,8 @@ </output> <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.9"/> </test> - <test> - <!-- test 6 --> + <test expect_num_outputs="2"> + <!-- test 7 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.subsample"/> @@ -402,8 +405,8 @@ </output> <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 7 --> + <test expect_num_outputs="2"> + <!-- test 8 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.subsample"/> @@ -425,8 +428,8 @@ </output> <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 8 --> + <test expect_num_outputs="2"> + <!-- test 9 --> <param name="adata" value="random-randint.h5ad" /> <conditional name="method"> <param name="method" value="pp.downsample_counts"/> @@ -461,7 +464,7 @@ `max_counts`, `max_genes` per call. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_cells.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_cells.html>`__ Filter genes based on number of cells or counts (`pp.filter_genes`) @@ -475,14 +478,14 @@ `max_counts`, `max_cells` per call. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_genes.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_genes.html>`__ Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`) ========================================================================================================================================================== More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.filter_rank_genes_groups.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__ Annotate highly variable genes (`pp.highly_variable_genes`) @@ -497,7 +500,7 @@ ====================================================================== More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.subsample.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.subsample.html>`__ Downsample counts (`pp.downsample_counts`) ========================================== @@ -506,7 +509,7 @@ has been implemented by M. D. Luecken. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.downsample_counts.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.downsample_counts.html>`__ ]]></help>