scanpy_inspect: inspect.xml comparison

comparison inspect.xml @ 11:6bd82ed14acd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d

author	iuc
date	Wed, 08 Nov 2023 14:48:14 +0000
parents	c5d3684f7c4c
children	3081ff5c84a3

comparison

equal deleted inserted replaced

-:c5d3684f7c4c
+:6bd82ed14acd
 <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">
 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling" help=""/>
 <param argument="random_state" type="integer" value="0" label="Random seed for sampling" help=""/>
 <xml name="random_state">
 <param argument="random_state" type="integer" value="" optional="true"
 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[
 @CMD@
 ]]></command>
 <param argument="c" type="float" value="1.0" label="Inverse of regularization strength"
 help="It must be a positive float. Like in support vector machines, smaller values specify stronger regularization."/>
 </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'"/>
 </repeat>
 <param argument="key" type="text" value="rank_genes_groups" label="Key in adata.uns where the rank_genes_groups output is stored"/>
 <when value="overlap_coef"/>
 <when value="jaccard"/>
 </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">
 <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
 label="Zero center?" help="If not, it omits zero-centering variables, which allows to handle sparse input efficiently."/>
 </inputs>
 <outputs>
 <expand macro="anndata_outputs"/>
 </outputs>
 <tests>
-<test>
+<test expect_num_outputs="2">
-<!-- test 0 -->
+<!-- test 1 -->
 <param name="adata" value="sparce_csr_matrix.h5ad" />
 <conditional name="method">
 <param name="method" value="pp.calculate_qc_metrics"/>
 <param name="expr_type" value="counts"/>
 <param name="var_type" value="genes"/>
 <has_text_matching expression="qc_vars=\['mito', 'negative'\]" />
 </assert_contents>
 </output>
 <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 1 -->
+<!-- test 2 -->
 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
 <conditional name="method">
 <param name="method" value="pp.neighbors"/>
 <param name="n_neighbors" value="15"/>
 <param name="knn" value="True"/>
 <assert_contents>
 <has_h5_keys keys="X, obs, obsm, uns, var" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 2 -->
+<!-- test 3 -->
 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
 <conditional name="method">
 <param name="method" value="pp.neighbors"/>
 <param name="n_neighbors" value="15"/>
 <param name="knn" value="True"/>
 <has_text_matching expression="metric='braycurtis'"/>
 </assert_contents>
 </output>
 <output name="anndata_out" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 3 -->
+<!-- test 4 -->
 <param name="adata" value="krumsiek11.h5ad" />
 <conditional name="method">
 <param name="method" value="tl.score_genes"/>
 <param name="gene_list" value="Gata2, Fog1"/>
 <param name="ctrl_size" value="2"/>
 <has_text_matching expression="copy=False" />
 </assert_contents>
 </output>
 <output name="anndata_out" file="tl.score_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 4 -->
+<!-- test 5 -->
 <param name="adata" value="krumsiek11.h5ad" />
 <conditional name="method">
 <param name="method" value="tl.score_genes_cell_cycle"/>
 <conditional name='s_genes'>
 <param name="format" value="text"/>
 <has_text_matching expression="use_raw=False"/>
 </assert_contents>
 </output>
 <output name="anndata_out" file="tl.score_genes_cell_cycle.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 5 -->
+<!-- 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>
 <param name="n_genes" value="100"/>
 <conditional name="tl_rank_genes_groups_method">
 </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=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'"/>
 <has_text_matching expression="corr_method='benjamini-hochberg'"/>
 </assert_contents>
 </output>
 <output name="anndata_out" file="tl.rank_genes_groups.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 6 -->
+<!-- test 7 -->
 <param name="adata" value="pbmc68k_reduced.h5ad" />
 <conditional name="method">
 <param name="method" value="tl.rank_genes_groups"/>
 <param name="groupby" value="louvain"/>
 <param name="use_raw" value="True"/>
 <assert_contents>
 <has_h5_keys keys="X, obs, obsm, raw/X, raw/var, uns, var" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 7 -->
+<!-- test 8 -->
 <param name="adata" value="pbmc68k_reduced.h5ad" />
 <conditional name="method">
 <param name="method" value="tl.rank_genes_groups"/>
 <param name="groupby" value="louvain"/>
 <param name="use_raw" value="True"/>
 <assert_contents>
 <has_h5_keys keys="X, obs, obsm, raw/X, raw/var, uns, var" />
 </assert_contents>
 </output>
 </test>
-<!--<test>
+<!-- test expect_num_outputs="2">
-< test 9 >
+< test 9  tl.marker_gene_overlap function was commented because inpace=True does not work>
-<param name="adata" value="tl.rank_genes_groups.louvain.neighbors.pca.pbmc68k_reduced.h5ad" />
+<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">
 <param name="key" value="CD4 T cells"/>
 <param name="value" value="IL7R"/>
 <repeat name="reference_markers">
 <param name="key" value="B cells"/>
 <param name="value" value="MS4A1"/>
 </repeat>
 <conditional name="overlap">
-<param argument="method" value="overlap_count"/>
+<param name="method" value="overlap_count"/>
-<param argument="normalize" value="None"/>
+<param name="normalize" value="None"/>
 </conditional>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="tl.marker_gene_overlap"/>
 <has_text_matching expression="key='rank_genes_groups'"/>
 <has_text_matching expression="method='overlap_count'"/>
 </assert_stdout>
+<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"/>
+</conditional>
+<section name="advanced_common">
+<param name="show_log" value="true" />
+</section>
+<output name="hidden_output">
+<assert_contents>
+<has_text_matching expression="sc.pp.log1p"/>
+</assert_contents>
+</output>
 <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
-</test>-->
+</test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 8 -->
+<!-- test 11 -->
-<param name="adata" value="krumsiek11.h5ad" />
-<conditional name="method">
-<param name="method" value="pp.log1p"/>
-</conditional>
-<section name="advanced_common">
-<param name="show_log" value="true" />
-</section>
-<output name="hidden_output">
-<assert_contents>
-<has_text_matching expression="sc.pp.log1p"/>
-</assert_contents>
-</output>
-<output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
-</test>
-<test>
-<!-- test 9 -->
 <param name="adata" value="krumsiek11.h5ad" />
 <conditional name="method">
 <param name="method" value="pp.scale"/>
 <param name="zero_center" value="true"/>
 </conditional>
 <has_text_matching expression="zero_center=True"/>
 </assert_contents>
 </output>
 <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 10 -->
+<!-- test 12 -->
 <param name="adata" value="krumsiek11.h5ad" />
 <conditional name="method">
 <param name="method" value="pp.scale"/>
 <param name="zero_center" value="true"/>
 <param name="max_value" value="10"/>
 <has_text_matching expression="max_value=10.0"/>
 </assert_contents>
 </output>
 <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 11 -->
+<!-- test 13 -->
 <param name="adata" value="krumsiek11.h5ad" />
 <conditional name="method">
 <param name="method" value="pp.sqrt"/>
 </conditional>
 <section name="advanced_common">
 - mean_{expr_type} (e.g. "mean counts", mean expression over all cells)
 - n_cells_by_{expr_type} (e.g. "n_cells_by_counts", number of cells this expression is measured in)
 - 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`
 ==================================================================
 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),
 - Distances for each pair of neighbors (distances)
 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`
 ============================================
 The score is the average expression of a set of genes subtracted with the
 This reproduces the approach in Seurat (Satija et al, 2015) and has been implemented
 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`
 =========================================================
 Given two lists of genes associated to S phase and G2M phase, calculates
 scores and assigns a cell cycle phase (G1, S or G2M). See
 `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`
 ==================================================================
 The returned AnnData object contains:
 - Ajusted p-values
 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`)
 ============================================================================================================
 Logarithmize the data matrix (`pp.log1p`)
 =========================================
 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`)
 ====================================================
 `X = sqrt(X)`

Mercurial > repos > iuc > scanpy_inspect

comparison inspect.xml @ 11:6bd82ed14acd draft