Mercurial > repos > iuc > scanpy_inspect
changeset 6:5e9171dc8244 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author | iuc |
---|---|
date | Thu, 20 Feb 2020 08:25:37 -0500 |
parents | 08192eebb47d |
children | 6c145a6868cc |
files | inspect.xml macros.xml |
diffstat | 2 files changed, 196 insertions(+), 118 deletions(-) [+] |
line wrap: on
line diff
--- a/inspect.xml Mon Feb 10 05:29:16 2020 -0500 +++ b/inspect.xml Thu Feb 20 08:25:37 2020 -0500 @@ -461,13 +461,14 @@ </when> <when value="pp.sqrt"/> </conditional> + <expand macro="inputs_common_advanced"/> </inputs> <outputs> <expand macro="anndata_outputs"/> </outputs> <tests> <test> - <!-- test 1 --> + <!-- test 0 --> <param name="adata" value="sparce_csr_matrix.h5ad" /> <conditional name="method"> <param name="method" value="pp.calculate_qc_metrics"/> @@ -476,16 +477,21 @@ <param name="qc_vars" value="mito,negative"/> <param name="percent_top" value=""/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.calculate_qc_metrics" /> - <has_text_matching expression="expr_type='counts'" /> - <has_text_matching expression="var_type='genes'" /> - <has_text_matching expression="qc_vars=\['mito', 'negative'\]" /> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.calculate_qc_metrics" /> + <has_text_matching expression="expr_type='counts'" /> + <has_text_matching expression="var_type='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 2 --> + <!-- test 1 --> <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" /> <conditional name="method"> <param name="method" value="pp.neighbors"/> @@ -495,14 +501,19 @@ <param name="pp_neighbors_method" value="umap"/> <param name="metric" value="euclidean"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.neighbors"/> - <has_text_matching expression="n_neighbors=15"/> - <has_text_matching expression="knn=True"/> - <has_text_matching expression="random_state=0"/> - <has_text_matching expression="method='umap'"/> - <has_text_matching expression="metric='euclidean'"/> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.neighbors"/> + <has_text_matching expression="n_neighbors=15"/> + <has_text_matching expression="knn=True"/> + <has_text_matching expression="random_state=0"/> + <has_text_matching expression="method='umap'"/> + <has_text_matching expression="metric='euclidean'"/> + </assert_contents> + </output> <output name="anndata_out" file="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"> <assert_contents> <has_h5_keys keys="X, obs, obsm, uns, var" /> @@ -510,7 +521,7 @@ </output> </test> <test> - <!-- test 3 --> + <!-- test 2 --> <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" /> <conditional name="method"> <param name="method" value="pp.neighbors"/> @@ -519,18 +530,23 @@ <param name="pp_neighbors_method" value="gauss"/> <param name="metric" value="braycurtis"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.neighbors"/> - <has_text_matching expression="n_neighbors=15"/> - <has_text_matching expression="knn=True"/> - <has_text_matching expression="random_state=0"/> - <has_text_matching expression="method='gauss'"/> - <has_text_matching expression="metric='braycurtis'"/> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.neighbors"/> + <has_text_matching expression="n_neighbors=15"/> + <has_text_matching expression="knn=True"/> + <has_text_matching expression="random_state=0"/> + <has_text_matching expression="method='gauss'"/> + <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 4 --> + <!-- test 3 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="tl.score_genes"/> @@ -541,20 +557,25 @@ <param name="use_raw" value="False"/> <param name="score_name" value="score"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.tl.score_genes" /> - <has_text_matching expression="gene_list=\['Gata2', 'Fog1'\]" /> - <has_text_matching expression="ctrl_size=2" /> - <has_text_matching expression="score_name='score'" /> - <has_text_matching expression="n_bins=2" /> - <has_text_matching expression="random_state=2" /> - <has_text_matching expression="use_raw=False" /> - <has_text_matching expression="copy=False" /> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.tl.score_genes" /> + <has_text_matching expression="gene_list=\['Gata2', 'Fog1'\]" /> + <has_text_matching expression="ctrl_size=2" /> + <has_text_matching expression="score_name='score'" /> + <has_text_matching expression="n_bins=2" /> + <has_text_matching expression="random_state=2" /> + <has_text_matching expression="use_raw=False" /> + <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 5 --> + <!-- test 4 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="tl.score_genes_cell_cycle"/> @@ -570,18 +591,23 @@ <param name="random_state" value="1"/> <param name="use_raw" value="False"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.tl.score_genes_cell_cycle"/> - <has_text_matching expression="s_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> - <has_text_matching expression="g2m_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> - <has_text_matching expression="n_bins=2"/> - <has_text_matching expression="random_state=1"/> - <has_text_matching expression="use_raw=False"/> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.tl.score_genes_cell_cycle"/> + <has_text_matching expression="s_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> + <has_text_matching expression="g2m_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> + <has_text_matching expression="n_bins=2"/> + <has_text_matching expression="random_state=1"/> + <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 6 --> + <!-- test 5 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="tl.rank_genes_groups"/> @@ -596,19 +622,24 @@ <param name="corr_method" value="benjamini-hochberg"/> </conditional> </conditional> - <assert_stdout> - <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="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_stdout> + <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=True"/> + <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 7 --> + <!-- test 6 --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <conditional name="method"> <param name="method" value="tl.rank_genes_groups"/> @@ -630,21 +661,26 @@ <param name="c" value="1.0"/> </conditional> </conditional> - <assert_stdout> - <has_text_matching expression="sc.tl.rank_genes_groups"/> - <has_text_matching expression="groupby='louvain'"/> - <has_text_matching expression="use_raw=True"/> - <has_text_matching expression="reference='rest'"/> - <has_text_matching expression="n_genes=100"/> - <has_text_matching expression="method='logreg'"/> - <has_text_matching expression="solver='newton-cg'"/> - <has_text_matching expression="penalty='l2'"/> - <has_text_matching expression="fit_intercept=True"/> - <has_text_matching expression="max_iter=100"/> - <has_text_matching expression="multi_class='auto'"/> - <has_text_matching expression="tol=0.0001"/> - <has_text_matching expression="C=1.0"/> - </assert_stdout> + <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='louvain'"/> + <has_text_matching expression="use_raw=True"/> + <has_text_matching expression="reference='rest'"/> + <has_text_matching expression="n_genes=100"/> + <has_text_matching expression="method='logreg'"/> + <has_text_matching expression="solver='newton-cg'"/> + <has_text_matching expression="penalty='l2'"/> + <has_text_matching expression="fit_intercept=True"/> + <has_text_matching expression="max_iter=100"/> + <has_text_matching expression="multi_class='auto'"/> + <has_text_matching expression="tol=0.0001"/> + <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"> <assert_contents> <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" /> @@ -652,7 +688,7 @@ </output> </test> <test> - <!-- test 8 --> + <!-- test 7 --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <conditional name="method"> <param name="method" value="tl.rank_genes_groups"/> @@ -680,21 +716,26 @@ <param name="c" value="1.0"/> </conditional> </conditional> - <assert_stdout> - <has_text_matching expression="sc.tl.rank_genes_groups"/> - <has_text_matching expression="groupby='louvain'"/> - <has_text_matching expression="use_raw=True"/> - <has_text_matching expression="reference='rest'"/> - <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"/> - </assert_stdout> + <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='louvain'"/> + <has_text_matching expression="use_raw=True"/> + <has_text_matching expression="reference='rest'"/> + <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"/> + </assert_contents> + </output> <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"> <assert_contents> <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" /> @@ -731,53 +772,73 @@ <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test>--> <test> - <!-- test 9 --> + <!-- test 8 --> <param name="adata" value="krumsiek11.h5ad" /> <conditional name="method"> <param name="method" value="pp.log1p"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.log1p"/> - </assert_stdout> + <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> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.scale"/> + <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 10 --> <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"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.scale"/> - <has_text_matching expression="zero_center=True"/> - </assert_stdout> - <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.scale"/> + <has_text_matching expression="zero_center=True"/> + <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 11 --> <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"/> - </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.scale"/> - <has_text_matching expression="zero_center=True"/> - <has_text_matching expression="max_value=10.0"/> - </assert_stdout> - <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> - </test> - <test> - <!-- test 12 --> - <param name="adata" value="krumsiek11.h5ad" /> - <conditional name="method"> <param name="method" value="pp.sqrt"/> </conditional> - <assert_stdout> - <has_text_matching expression="sc.pp.sqrt"/> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sc.pp.sqrt"/> + </assert_contents> + </output> <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> </test> </tests> @@ -889,4 +950,4 @@ `X = sqrt(X)` ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>
--- a/macros.xml Mon Feb 10 05:29:16 2020 -0500 +++ b/macros.xml Thu Feb 20 08:25:37 2020 -0500 @@ -21,12 +21,17 @@ </xml> <token name="@CMD@"><![CDATA[ cp '$adata' 'anndata.h5ad' && -cat '$script_file' && -python '$script_file' && -ls . +cat '$script_file' > '$hidden_output' && +python '$script_file' >> '$hidden_output' && +ls . >> '$hidden_output' && +touch 'anndata_info.txt' && +cat 'anndata_info.txt' @CMD_prettify_stdout@ ]]> </token> <token name="@CMD_imports@"><![CDATA[ +import sys +sys.stderr = open('$hidden_output', 'a') + import scanpy as sc import pandas as pd import numpy as np @@ -39,13 +44,25 @@ adata = sc.read('anndata.h5ad') ]]> </token> + <xml name="inputs_common_advanced"> + <section name="advanced_common" title="Advanced Options" expanded="false"> + <param name="show_log" type="boolean" checked="false" label="Output Log?" /> + </section> + </xml> <xml name="anndata_outputs"> <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> + <data name="hidden_output" format="txt" label="Log file" > + <filter>advanced_common['show_log']</filter> + </data> </xml> <token name="@CMD_anndata_write_outputs@"><![CDATA[ adata.write('anndata.h5ad') +with open('anndata_info.txt','w', encoding='utf-8') as ainfo: + print(adata, file=ainfo) ]]> </token> + <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g' + ]]></token> <xml name="svd_solver"> <param name="svd_solver" type="select" label="SVD solver to use" help=""> <option value="auto">Automatically chosen depending on the size of the problem</option>