Mercurial > repos > iuc > scanpy_inspect
changeset 8:9d33775ec67d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 12:59:22 +0000 |
| parents | 6c145a6868cc |
| children | e4c99c83dfbf |
| files | inspect.xml macros.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png test-data/pl.scatter.umap.pbmc68k_reduced.png test-data/pl.stacked_violin.krumsiek11.png test-data/pl.violin.pbmc68k_reduced_custom.png test-data/pp.highly_variable_genes.seurat.blobs.h5ad test-data/pp.recipe_seurat.recipe_zheng17.h5ad test-data/pp.recipe_zheng17.random-randint.h5ad test-data/tl.rank_genes_groups.krumsiek11.h5ad |
| diffstat | 11 files changed, 11 insertions(+), 19 deletions(-) [+] |
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--- a/inspect.xml Wed May 20 16:10:30 2020 -0400 +++ b/inspect.xml Tue Mar 16 12:59:22 2021 +0000 @@ -232,12 +232,12 @@ #else if $method.method == "pp.log1p" sc.pp.log1p( - data=adata, + adata, copy=False) #else if $method.method == "pp.scale" sc.pp.scale( - data=adata, + adata, zero_center=$method.zero_center, #if $method.max_value max_value=$method.max_value, @@ -246,7 +246,7 @@ #else if $method.method == "pp.sqrt" sc.pp.sqrt( - data=adata, + adata, copy=False) #end if @@ -707,9 +707,9 @@ <has_text_matching expression="C=1.0"/> </assert_contents> </output> - <output name="anndata_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size"> + <output name="anndata_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"> <assert_contents> - <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" /> + <has_h5_keys keys="X, obs, obsm, raw/X, raw/var, uns, var" /> </assert_contents> </output> </test> @@ -762,9 +762,9 @@ <has_text_matching expression="C=1.0"/> </assert_contents> </output> - <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"> + <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"> <assert_contents> - <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" /> + <has_h5_keys keys="X, obs, obsm, raw/X, raw/var, uns, var" /> </assert_contents> </output> </test>
--- a/macros.xml Wed May 20 16:10:30 2020 -0400 +++ b/macros.xml Tue Mar 16 12:59:22 2021 +0000 @@ -1,13 +1,12 @@ <macros> - <token name="@version@">1.4.4.post1</token> + <token name="@version@">1.7.1</token> <token name="@profile@">19.01</token> - <token name="@galaxy_version@"><![CDATA[@version@+galaxy3]]></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="2.9.0">h5py</requirement> - <requirement type="package" version="0.7.0">leidenalg</requirement> + <requirement type="package" version="0.8.3">leidenalg</requirement> <yield /> </requirements> </xml> @@ -29,9 +28,6 @@ ]]> </token> <token name="@CMD_imports@"><![CDATA[ -import sys -sys.stderr = open('$hidden_output', 'a') - import scanpy as sc import pandas as pd import numpy as np @@ -768,9 +764,6 @@ <param argument="color" type="select" label="Color for all of the elements" help=""> <expand macro="matplotlib_color"/> </param> - <param argument="palette" type="select" label="Colors to use for the different levels of the hue variable" help=""> - <expand macro="matplotlib_pyplot_colormap"/> - </param> <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/> </section> </xml> @@ -781,7 +774,6 @@ #end if linewidth=$method.seaborn_violinplot.linewidth, color='$method.seaborn_violinplot.color', - palette='$method.seaborn_violinplot.palette', saturation=$method.seaborn_violinplot.saturation ]]></token> <xml name="param_color"> @@ -1005,7 +997,7 @@ <option value="eq_tree">eq_tree: Equally spaced tree</option> </xml> <xml name="param_layout"> - <param argument="layout" type="select" label="Plotting layout" help=""> + <param argument="layout" type="select" label="Plotting layout" optional="false" help=""> <expand macro="options_layout"/> </param> </xml>