Mercurial > repos > iuc > scanpy_inspect
changeset 11:6bd82ed14acd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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--- a/inspect.xml Wed Sep 22 21:14:32 2021 +0000 +++ b/inspect.xml Wed Nov 08 14:48:14 2023 +0000 @@ -1,6 +1,5 @@ <tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@"> <description> with scanpy</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> <xml name="score_genes_params"> @@ -51,6 +50,7 @@ label="The seed of the pseudo random number generator to use when shuffling the data" help=""/> </xml> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ @@ -453,7 +453,8 @@ </when> </conditional> </when> - <!--<when value="tl.marker_gene_overlap"> + <!-- With inplace=True, NotImplementedError: Writing Pandas dataframes to h5ad is currently under development. Please use `inplace=False`. --> + <!-- <when value="tl.marker_gene_overlap"> <repeat name="reference_markers" title="Marker genes"> <param name="key" type="text" value="" label="Cell identity name" help=""/> <param name="values" type="text" value="" label="List of genes" help="Comma-separated names from 'var'"/> @@ -477,7 +478,7 @@ </conditional> <param argument="top_n_markers" type="integer" optional="true" label="Number of top data-derived marker genes to use" help="By default all calculated marker genes are used. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/> <param argument="adj_pval_threshold" type="float" optional="true" label="Significance threshold on the adjusted p-values to select marker genes" help=" This can only be used when adjusted p-values are calculated by 'tl.rank_genes_groups'. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/> - <param argument="key_added" type="text" value="" optional="true" label="Key that will contain the marker overlap scores in 'uns'"/> + <param argument="key_added" type="text" value="marker_gene_overlap" optional="true" label="Key that will contain the marker overlap scores in 'uns'"/> </when>--> <when value="pp.log1p"/> <when value="pp.scale"> @@ -494,8 +495,8 @@ <expand macro="anndata_outputs"/> </outputs> <tests> - <test> - <!-- test 0 --> + <test expect_num_outputs="2"> + <!-- test 1 --> <param name="adata" value="sparce_csr_matrix.h5ad" /> <conditional name="method"> <param name="method" value="pp.calculate_qc_metrics"/> @@ -517,8 +518,8 @@ </output> <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 1 --> + <test expect_num_outputs="2"> + <!-- test 2 --> <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" /> <conditional name="method"> <param name="method" value="pp.neighbors"/> @@ -547,8 +548,8 @@ </assert_contents> </output> </test> - <test> - <!-- test 2 --> + <test expect_num_outputs="2"> + <!-- test 3 --> <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" /> <conditional name="method"> <param name="method" value="pp.neighbors"/> @@ -572,8 +573,8 @@ </output> <output name="anndata_out" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 3 --> + <test expect_num_outputs="2"> + <!-- test 4 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="tl.score_genes"/> @@ -601,8 +602,8 @@ </output> <output name="anndata_out" file="tl.score_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 4 --> + <test expect_num_outputs="2"> + <!-- test 5 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="tl.score_genes_cell_cycle"/> @@ -633,13 +634,13 @@ </output> <output name="anndata_out" file="tl.score_genes_cell_cycle.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 5 --> + <test expect_num_outputs="2"> + <!-- test 6 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="tl.rank_genes_groups"/> <param name="groupby" value="cell_type"/> - <param name="use_raw" value="True"/> + <param name="use_raw" value="False"/> <conditional name="ref"> <param name="rest" value="rest"/> </conditional> @@ -656,7 +657,7 @@ <assert_contents> <has_text_matching expression="sc.tl.rank_genes_groups"/> <has_text_matching expression="groupby='cell_type'"/> - <has_text_matching expression="use_raw=True"/> + <has_text_matching expression="use_raw=False"/> <has_text_matching expression="reference='rest'"/> <has_text_matching expression="n_genes=100"/> <has_text_matching expression="method='t-test_overestim_var'"/> @@ -665,8 +666,8 @@ </output> <output name="anndata_out" file="tl.rank_genes_groups.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 6 --> + <test expect_num_outputs="2"> + <!-- test 7 --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <conditional name="method"> <param name="method" value="tl.rank_genes_groups"/> @@ -714,8 +715,8 @@ </assert_contents> </output> </test> - <test> - <!-- test 7 --> + <test expect_num_outputs="2"> + <!-- test 8 --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <conditional name="method"> <param name="method" value="tl.rank_genes_groups"/> @@ -769,9 +770,9 @@ </assert_contents> </output> </test> - <!--<test> - < test 9 > - <param name="adata" value="tl.rank_genes_groups.louvain.neighbors.pca.pbmc68k_reduced.h5ad" /> + <!-- test expect_num_outputs="2"> + < test 9 tl.marker_gene_overlap function was commented because inpace=True does not work> + <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" /> <conditional name="method"> <param name="method" value="tl.marker_gene_overlap"/> <repeat name="reference_markers"> @@ -787,8 +788,8 @@ <param name="value" value="MS4A1"/> </repeat> <conditional name="overlap"> - <param argument="method" value="overlap_count"/> - <param argument="normalize" value="None"/> + <param name="method" value="overlap_count"/> + <param name="normalize" value="None"/> </conditional> </conditional> <assert_stdout> @@ -796,10 +797,10 @@ <has_text_matching expression="key='rank_genes_groups'"/> <has_text_matching expression="method='overlap_count'"/> </assert_stdout> - <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> - </test>--> - <test> - <!-- test 8 --> + <output name="anndata_out" file="tl.marker_gene_overlap.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size"/> + </test> --> + <test expect_num_outputs="2"> + <!-- test 10 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.log1p"/> @@ -814,8 +815,8 @@ </output> <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 9 --> + <test expect_num_outputs="2"> + <!-- test 11 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.scale"/> @@ -832,8 +833,8 @@ </output> <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 10 --> + <test expect_num_outputs="2"> + <!-- test 12 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.scale"/> @@ -852,8 +853,8 @@ </output> <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> - <!-- test 11 --> + <test expect_num_outputs="2"> + <!-- test 13 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.sqrt"/> @@ -892,7 +893,7 @@ - pct_dropout_by_{expr_type} (e.g. "pct_dropout_by_counts", percentage of cells this feature does not appear in) More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.calculate_qc_metrics.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.calculate_qc_metrics.html>`__ Compute a neighborhood graph of observations, using `pp.neighbors` ================================================================== @@ -911,7 +912,7 @@ This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.neighbors.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.neighbors.html>`__ Score a set of genes, using `tl.score_genes` ============================================ @@ -924,7 +925,7 @@ for Scanpy by Davide Cittaro. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.score_genes.html>`__ Score cell cycle genes, using `tl.score_genes_cell_cycle` ========================================================= @@ -934,7 +935,7 @@ `score_genes` for more explanation. More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes_cell_cycle.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__ Rank genes for characterizing groups, using `tl.rank_genes_groups` ================================================================== @@ -950,7 +951,7 @@ This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.rank_genes_groups.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.rank_genes_groups.html>`__ Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`) @@ -963,13 +964,13 @@ ========================================= More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.log1p.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.log1p.html>`__ Scale data to unit variance and zero mean (`pp.scale`) ====================================================== More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.scale.html>`__ +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.scale.html>`__ Computes the square root the data matrix (`pp.sqrt`) ====================================================
--- a/macros.xml Wed Sep 22 21:14:32 2021 +0000 +++ b/macros.xml Wed Nov 08 14:48:14 2023 +0000 @@ -1,12 +1,16 @@ <macros> - <token name="@version@">1.7.1</token> - <token name="@profile@">19.01</token> + <token name="@version@">1.9.6</token> + <token name="@profile@">22.05</token> <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> <xml name="requirements"> <requirements> <requirement type="package" version="@version@">scanpy</requirement> - <requirement type="package" version="2.0.17">loompy</requirement> - <requirement type="package" version="0.8.3">leidenalg</requirement> + <requirement type="package" version="3.0.6">loompy</requirement> + <requirement type="package" version="0.10.1">leidenalg</requirement> + <requirement type="package" version="0.8.1">louvain</requirement> + <requirement type="package" version="1.5.3">pandas</requirement> + <requirement type="package" version="3.7">matplotlib</requirement> + <requirement type="package" version="0.12.2">seaborn</requirement> <yield /> </requirements> </xml> @@ -15,9 +19,15 @@ <xref type="bio.tools">scanpy</xref> </xrefs> </xml> + <xml name="creators"> + <creator> + <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" /> + </creator> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-017-1382-0</citation> + <citation type="doi">10.1093/gigascience/giaa102</citation> </citations> </xml> <xml name="version_command"> @@ -56,7 +66,7 @@ <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> </xml> <token name="@CMD_read_inputs@"><![CDATA[ -adata = sc.read('anndata.h5ad') +adata = sc.read_h5ad('anndata.h5ad') ]]> </token> <xml name="inputs_common_advanced"> @@ -66,12 +76,12 @@ </xml> <xml name="anndata_outputs"> <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> - <data name="hidden_output" format="txt" label="Log file" > + <data name="hidden_output" format="txt" label="Log file" > <filter>advanced_common['show_log']</filter> </data> </xml> <token name="@CMD_anndata_write_outputs@"><![CDATA[ -adata.write('anndata.h5ad') +adata.write_h5ad('anndata.h5ad') with open('anndata_info.txt','w', encoding='utf-8') as ainfo: print(adata, file=ainfo) ]]> @@ -875,7 +885,7 @@ </xml> <xml name="param_color_map"> <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> - <option value="None">Default</option> + <option value="" >Default</option> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> @@ -979,7 +989,7 @@ @CMD_param_legend_fontsize@ legend_fontweight='$method.plot.legend_fontweight', @CMD_param_size@ - #if str($method.plot.color_map) != 'None' + #if str($method.plot.color_map) != '' color_map='$method.plot.color_map', #end if #if str($method.plot.palette) != ''
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