Mercurial > repos > iuc > scanpy_cluster_reduce_dimension
changeset 8:35bc2eb568ed draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 13:03:42 +0000 |
| parents | b2df381a6004 |
| children | 3e4e1cf73d98 |
| files | cluster_reduce_dimension.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, 10 insertions(+), 21 deletions(-) [+] |
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--- a/cluster_reduce_dimension.xml Wed May 20 16:11:15 2020 -0400 +++ b/cluster_reduce_dimension.xml Tue Mar 16 13:03:42 2021 +0000 @@ -3,7 +3,7 @@ <macros> <import>macros.xml</import> <xml name="pca_inputs"> - <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/> + <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help="If the value is larger than the number of observations the number of observations is used instead"/> <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""> <expand macro="sanitize_query" /> </param> @@ -46,7 +46,7 @@ ]]></token> <token name="@CMD_pca_params@"><![CDATA[ data=adata, - n_comps=$method.n_comps, + n_comps=min($method.n_comps, adata.n_vars), dtype='$method.dtype', copy=False, chunked=$method.pca.chunked, @@ -61,7 +61,7 @@ ]]></token> </macros> <expand macro="requirements"> - <requirement type="package" version="0.6.1">louvain</requirement> + <requirement type="package" version="0.7.0">louvain</requirement> </expand> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ @@ -104,7 +104,7 @@ #else if $method.method == 'tl.diffmap' sc.tl.diffmap( adata=adata, - n_comps=$method.n_comps, + n_comps=min($method.n_comps, adata.n_vars), copy =False) #else if $method.method == 'tl.tsne' @@ -372,7 +372,6 @@ <output name="hidden_output"> <assert_contents> <has_text_matching expression="sc.pp.pca"/> - <has_text_matching expression="n_comps=50"/> <has_text_matching expression="dtype='float32'"/> <has_text_matching expression="copy=False"/> <has_text_matching expression="chunked=False"/> @@ -382,7 +381,7 @@ <has_text_matching expression="use_highly_variable=False"/> </assert_contents> </output> - <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/> </test> <!--<test> < test 3 > @@ -431,7 +430,6 @@ <output name="hidden_output"> <assert_contents> <has_text_matching expression="sc.tl.pca"/> - <has_text_matching expression="n_comps=50"/> <has_text_matching expression="dtype='float32'"/> <has_text_matching expression="copy=False"/> <has_text_matching expression="chunked=False"/> @@ -440,7 +438,7 @@ <has_text_matching expression="use_highly_variable=False"/> </assert_contents> </output> - <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> + <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/> </test> <test> <!-- test 3 --> @@ -455,7 +453,6 @@ <output name="hidden_output"> <assert_contents> <has_text_matching expression="sc.tl.diffmap"/> - <has_text_matching expression="n_comps=15"/> </assert_contents> </output> <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
--- a/macros.xml Wed May 20 16:11:15 2020 -0400 +++ b/macros.xml Tue Mar 16 13:03:42 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>