| Previous changeset 17:18262103fa61 (2024-09-14) Next changeset 19:4338bf96809e (2024-10-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634 |
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modified:
inspect.xml macros.xml |
| b |
| diff -r 18262103fa61 -r d1cd8c147809 inspect.xml --- a/inspect.xml Sat Sep 14 12:45:03 2024 +0000 +++ b/inspect.xml Thu Sep 19 06:43:47 2024 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> +<tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <macros> <import>macros.xml</import> <xml name="params_score_genes"> @@ -146,7 +146,7 @@ use_raw=$method.use_raw, #if str($method.groups) != '': #set $group=[x.strip() for x in str($method.groups).split(',')] - groups='$group', + groups=$group, #end if #if str($method.layer) != '': layer='$method.layer', @@ -446,7 +446,7 @@ <expand macro="fit_intercept"/> <expand macro="max_iter"/> <expand macro="multi_class"/> - </when> + </when> <when value="newton-cg"> <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/> <expand macro="fit_intercept"/> @@ -560,8 +560,7 @@ <expand macro="anndata_outputs"/> </outputs> <tests> - - <!-- test 1 --> +<!-- test 1 --> <test expect_num_outputs="2"> <param name="adata" value="sparce_csr_matrix.h5ad"/> <conditional name="method"> @@ -614,7 +613,7 @@ </assert_contents> </output> </test> - + <!-- test 3 --> <test expect_num_outputs="2"> <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad"/> @@ -851,10 +850,61 @@ <has_h5_keys keys="uns/rank_genes_groups"/> </assert_contents> </output> - </test> + </test> <!-- test 10 --> <test expect_num_outputs="2"> + <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="groups" value="Ery"/> + <conditional name="ref"> + <param name="rest" value="group_id"/> + <param name="reference" value="Mk"/> + </conditional> + <param name="n_genes" value="100"/> + <conditional name="tl_rank_genes_groups_method"> + <param name="method" value="logreg"/> + <conditional name="solver"> + <param name="solver" value="liblinear"/> + <conditional name="penalty"> + <param name="penalty" value="l2"/> + <param name="random_state" value="1"/> + </conditional> + </conditional> + </conditional> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true"/> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.tl.rank_genes_groups"/> + <has_text_matching expression="groupby='cell_type'"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="n_genes=100"/> + <has_text_matching expression="method='logreg'"/> + <has_text_matching expression="solver='liblinear'"/> + <has_text_matching expression="penalty='l2'"/> + <has_text_matching expression="dual=False"/> + <has_text_matching expression="fit_intercept=True"/> + <has_text_matching expression="intercept_scaling=1.0"/> + <has_text_matching expression="tol=0.0001"/> + <has_text_matching expression="C=1.0"/> + <has_text_matching expression="groups=\['Ery'\]"/> + <has_text_matching expression="reference='Mk'"/> + </assert_contents> + </output> + <output name="anndata_out" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="uns/rank_genes_groups"/> + </assert_contents> + </output> + </test> + + <!-- test 11 --> + <test expect_num_outputs="2"> <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad"/> <conditional name="method"> <param name="method" value="tl.marker_gene_overlap"/> @@ -889,7 +939,7 @@ </output> </test> - <!-- test 11 --> + <!-- test 12 --> <test expect_num_outputs="2"> <param name="adata" value="krumsiek11.h5ad"/> <conditional name="method"> @@ -910,7 +960,7 @@ </output> </test> - <!-- test 12 --> + <!-- test 13 --> <test expect_num_outputs="2"> <param name="adata" value="krumsiek11.h5ad"/> <conditional name="method"> @@ -929,9 +979,10 @@ <assert_contents> <has_h5_keys keys="var/mean,var/std"/> </assert_contents> - </output> </test> + </output> + </test> - <!-- test 13 --> + <!-- test 14 --> <test expect_num_outputs="2"> <param name="adata" value="krumsiek11.h5ad"/> <conditional name="method"> @@ -955,7 +1006,7 @@ </output> </test> - <!-- test 14 --> + <!-- test 15 --> <test expect_num_outputs="2"> <param name="adata" value="random-randint.h5ad"/> <conditional name="method"> |
| b |
| diff -r 18262103fa61 -r d1cd8c147809 macros.xml --- a/macros.xml Sat Sep 14 12:45:03 2024 +0000 +++ b/macros.xml Thu Sep 19 06:43:47 2024 +0000 |
| [ |
| @@ -9,7 +9,7 @@ <requirement type="package" version="1.26.4">numpy</requirement> <requirement type="package" version="2.2.2">pandas</requirement> <requirement type="package" version="1.14.1">scipy</requirement> - <requirement type="package" version="0.14.2">statsmodels</requirement> + <requirement type="package" version="0.14.2">statsmodels</requirement> <yield /> </requirements> </xml> @@ -29,8 +29,8 @@ <citation type="doi">10.1093/gigascience/giaa102</citation> </citations> </xml> - - + + <!-- param macros --> <xml name="sanitize_query" token_validinitial="string.printable"> <sanitizer> @@ -45,7 +45,7 @@ <add value=","/> </valid> </sanitizer> - </xml> + </xml> <xml name="inputs_anndata"> <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> </xml> @@ -61,7 +61,7 @@ <data name="hidden_output" format="txt" label="Log file" > <filter>advanced_common['show_log']</filter> </data> - </xml> + </xml> <xml name="param_use_rep"> <param argument="use_rep" type="text" value="" optional="true" label="Use the indicated representation" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter"> <expand macro="sanitize_query"/> @@ -546,7 +546,7 @@ <!-- param macros --> - + <!-- command macros --> <xml name="version_command"> <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> @@ -936,7 +936,7 @@ #end if ]]> </token> - + <xml name="params_seaborn_violinplot"> <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot"> <param argument="bw_method" type="select" label="Name of a reference rule when computing the kernel bandwidth"> @@ -969,7 +969,7 @@ #end if saturation=$method.seaborn_violinplot.saturation, ]]></token> - + <xml name="param_color"> <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'"> <expand macro="sanitize_query"/> @@ -1017,7 +1017,7 @@ #end if ]]> </token> - + <xml name="param_legend_fontsize"> <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size"/> </xml> |