| Previous changeset 0:af821711b356 (2024-05-16) Next changeset 2:94ae400dde2f (2024-07-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f |
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modified:
dimension_reduction_clustering.xml macros.xml |
| b |
| diff -r af821711b356 -r 8f8bef61fd0b dimension_reduction_clustering.xml --- a/dimension_reduction_clustering.xml Thu May 16 13:15:57 2024 +0000 +++ b/dimension_reduction_clustering.xml Thu May 23 15:19:58 2024 +0000 |
| [ |
| b'@@ -18,127 +18,130 @@\n @CMD_read_inputs@\n \n #if $method.method == \'tl.spectral\'\n-\t#if $method.features\n+ #if $method.features\n with open(\'$method.features\') as f:\n-\tfeatures_mask = [x.lower().capitalize() == "True" for x in f.read().splitlines()]\n-\t#end if\n+ features_mask = [x.lower().capitalize() == "True" for x in f.read().splitlines()]\n+ #end if\n sa.tl.spectral(\n-\tadata,\n-\tn_comps = $method.n_comps,\n-\t#if $method.features\n-\tfeatures = features_mask,\n-\t#end if\n-\trandom_state = $method.random_state,\n-\t#if $method.sample_size\n-\tsample_size = $method.sample_size,\n-\t#end if\n-\tchunk_size = $method.chunk_size,\n-\tdistance_metric = \'$method.distance_metric\',\n-\tweighted_by_sd = $method.weighted_by_sd,\n-\tinplace = True\n+ adata,\n+ n_comps = $method.n_comps,\n+ #if $method.features\n+ features = features_mask,\n+ #end if\n+ random_state = $method.random_state,\n+ #if $method.sample_size\n+ sample_size = $method.sample_size,\n+ #end if\n+ chunk_size = $method.chunk_size,\n+ distance_metric = \'$method.distance_metric\',\n+ weighted_by_sd = $method.weighted_by_sd,\n+ inplace = True\n )\n \n #else if $method.method == \'tl.umap\'\n sa.tl.umap(\n-\tadata,\n-\tn_comps = $method.n_comps,\n-\t#if $method.use_dims != \'\'\n-\t #set $dims = ([x.strip() for x in str($method.use_dims).split(\',\')])\n-\tuse_dims=$dims,\n-\t#end if\n-\tuse_rep = \'$method.use_rep\',\n-\tkey_added = \'$method.key_added\',\n-\trandom_state = $method.random_state,\n-\tinplace = True\n+ adata,\n+ n_comps = $method.n_comps,\n+ #if $method.use_dims != \'\'\n+ #set $dims = ([x.strip() for x in str($method.use_dims).split(\',\')])\n+ use_dims=$dims,\n+ #end if\n+ use_rep = \'$method.use_rep\',\n+ key_added = \'$method.key_added\',\n+ random_state = $method.random_state,\n+ inplace = True\n )\n \n #else if $method.method == \'pp.knn\'\n sa.pp.knn(\n-\tadata,\n-\tn_neighbors = $method.n_neighbors,\n-\t#if $method.use_dims != \'\'\n-\t #set $dims = ([x.strip() for x in str($method.use_dims).split(\',\')])\n-\tuse_dims=$dims,\n-\t#end if\n-\tuse_rep = \'$method.use_rep\',\n-\tmethod = \'$method.algorithm\',\n-\tinplace = True,\n-\trandom_state = $method.random_state\n+ adata,\n+ n_neighbors = $method.n_neighbors,\n+ #if $method.use_dims != \'\'\n+ #set $dims = ([x.strip() for x in str($method.use_dims).split(\',\')])\n+ use_dims=$dims,\n+ #end if\n+ use_rep = \'$method.use_rep\',\n+ method = \'$method.algorithm\',\n+ inplace = True,\n+ random_state = $method.random_state\n )\n \n #else if $method.method == \'tl.dbscan\'\n sa.tl.dbscan(\n-\tadata,\n-\teps = $method.eps,\n-\tmin_samples = $method.min_samples,\n-\tleaf_size = $method.leaf_size,\n-\tuse_rep = \'$method.use_rep\',\n-\tkey_added = \'$method.key_added\'\n+ adata,\n+ eps = $method.eps,\n+ min_samples = $method.min_samples,\n+ leaf_size = $method.leaf_size,\n+ use_rep = \'$method.use_rep\',\n+ key_added = \'$method.key_added\'\n )\n \n #else if $method.method == \'tl.hdbscan\'\n sa.tl.hdbscan(\n-\tadata,\n-\tmin_cluster_size = $method.min_cluster_size,\n-\t#if $method.min_samples\n-\tmin_samples = $method.min_samples,\n-\t#end if\n-\tcluster_selection_epsilon = $method.cluster_selection_epsilon,\n-\talpha = $method.alpha,\n-\tcluster_selection_method = \'$method.cluster_selection_method\',\n-\trandom_state = $method.random_state,\n-\tuse_rep = \'$method.use_rep\',\n-\tkey_added = \'$method.key_added\'\n+ adata,\n+ min_cluster_size = $method.min_cluster_size,\n+ #if $method.min_samples\n+ min_samples = $method.min_samples,\n+ #end if\n+ cluster_selection_epsilon = $method.cluster_selection_epsilon,\n+ alpha = $method.alpha,\n+ cluster_selection_method = \'$method.cluster_selection_method\',\n+ random_state = $method.random_state,\n+ use_rep = \'$method.use_rep\',\n+ key_added = \'$method.key_added\'\n )\n \n #else if $method.method == \'tl.leiden\'\n sa.tl.leiden(\n-\tadata,\n-\tresolution = $method.resolution,\n-\tobjective_function = \'$method.objective_function\',\n-\tmin_cluster_size = $method.min_cluster_size,\n-\tn_iterations = $method.n_iterations,\n-\trando'..b'value="3"/>\n <param name="leaf_size" value="5"/>\n@@ -417,13 +450,13 @@\n <has_text_matching expression="key_added = \'dbscan\'"/>\n </assert_contents>\n </output>\n- <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.dbscan.pbmc_500_chr21.h5ad"/>\n+ <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.dbscan.pbmc_500_chr21.h5ad"/>\n </test>\n <test expect_num_outputs="2">\n <!-- tl.hdbscan -->\n <conditional name="method">\n <param name="method" value="tl.hdbscan"/>\n- <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>\n+ <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>\n <param name="min_cluster_size" value="3"/>\n <param name="min_samples" value="3"/>\n <param name="cluster_selection_method" value="eom"/>\n@@ -445,13 +478,13 @@\n <has_text_matching expression="key_added = \'hdbscan\'"/>\n </assert_contents>\n </output>\n- <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.hdbscan.pbmc_500_chr21.h5ad"/>\n+ <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.hdbscan.pbmc_500_chr21.h5ad"/>\n </test>\n <test expect_num_outputs="2">\n <!-- tl.aggregate_X -->\n <conditional name="method">\n <param name="method" value="tl.aggregate_X"/>\n- <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>\n+ <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>\n <param name="normalize" value="RPKM"/>\n </conditional>\n <section name="advanced_common">\n@@ -463,13 +496,13 @@\n <has_text_matching expression="normalize = \'RPKM\'"/>\n </assert_contents>\n </output>\n- <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.aggregate_X.pbmc_500_chr21.h5ad"/>\n+ <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.aggregate_X.pbmc_500_chr21.h5ad"/>\n </test>\n <test expect_num_outputs="2">\n <!-- tl.aggregate_cells -->\n <conditional name="method">\n <param name="method" value="tl.aggregate_cells"/>\n- <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>\n+ <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>\n <param name="use_rep" value="X_spectral"/>\n <param name="target_num_cells" value="5"/>\n <param name="min_cluster_size" value="3"/>\n@@ -489,7 +522,7 @@\n <has_text_matching expression="key_added = \'pseudo_cell\'"/>\n </assert_contents>\n </output>\n- <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.aggregate_cells.pbmc_500_chr21.h5ad"/>\n+ <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.aggregate_cells.pbmc_500_chr21.h5ad"/>\n </test>\n </tests>\n <help><![CDATA[\n' |
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| diff -r af821711b356 -r 8f8bef61fd0b macros.xml --- a/macros.xml Thu May 16 13:15:57 2024 +0000 +++ b/macros.xml Thu May 23 15:19:58 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.5.3</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">2.5.3</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.0</token> <xml name="requirements"> <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement> @@ -12,6 +12,9 @@ <requirement type="package" version="0.8.33">hdbscan</requirement> <requirement type="package" version="0.0.9">harmonypy</requirement> <requirement type="package" version="1.7.4">scanorama</requirement> + <requirement type="package" version="3.0.1">macs3</requirement> + <requirement type="package" version="0.70.16">multiprocess</requirement> + <requirement type="package" version="0.10.2">leidenalg</requirement> <yield /> </xml> @@ -23,8 +26,8 @@ <token name="@CMD@"><![CDATA[ cat '$script_file' > '$hidden_output' && python '$script_file' >> '$hidden_output' && - touch 'anndata_info.txt' && - cat 'anndata_info.txt' @CMD_prettify_stdout@ + touch 'anndata_info.txt' && + cat 'anndata_info.txt' @CMD_prettify_stdout@ ]]> </token> @@ -56,7 +59,7 @@ <xml name="dimentions_plot"> <param argument="width" type="integer" value="500" label="Width of the plot"/> - <param argument="height" type="integer" value="400" label="Height of the plot"/> + <param argument="height" type="integer" value="400" label="Height of the plot"/> </xml> <xml name="param_groupby"> @@ -66,11 +69,11 @@ </xml> <xml name="out_file"> - <param name="out_file" type="select" optional="true" label="Type of output file"> + <param name="out_file" type="select" optional="true" label="Type of output plot"> <option value="png" selected="true">PNG</option> <option value="svg">SVG</option> <option value="pdf">PDF</option> - </param> + </param> </xml> <token name="@CMD_anndata_write_outputs@"><![CDATA[ adata.write('anndata.h5ad') @@ -89,28 +92,28 @@ <expand macro="out_file"/> </xml> <xml name="param_shift"> - <param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/> - <param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/> + <param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/> + <param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/> </xml> <xml name="param_chunk_size" tokens="size"> - <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/> + <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/> + </xml> + <xml name="min_max_frag_size"> + <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/> + <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/> </xml> - <xml name="min_max_frag_size"> - <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/> - <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/> - </xml> - <xml name="params_data_integration"> - <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/> - <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation"> - <expand macro="sanitize_query"/> - </param> - <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider"> + <xml name="params_data_integration"> + <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/> + <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation"> + <expand macro="sanitize_query"/> + </param> + <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider"> <expand macro="sanitize_query" /> </param> - <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/> - </xml> + <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/> + </xml> <xml name="param_n_comps"> -s <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/> + <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/> </xml> <xml name="param_random_state"> <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/> @@ -126,12 +129,12 @@ </xml> <xml name="background"> <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background"> - <expand macro="sanitize_query"/> - </param> + <expand macro="sanitize_query"/> + </param> </xml> <xml name="mat"> <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/> - <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/> + <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/> </xml> <xml name="param_network"> <param argument="network" type="text" label="network"/> @@ -147,11 +150,11 @@ </citations> </xml> <xml name="render_plot_test"> - <param name="width" value="650"/> + <param name="width" value="650"/> <param name="height" value="450"/> </xml> <xml name="render_plot_matching_text"> - <has_text_matching expression="width = 650"/> + <has_text_matching expression="width = 650"/> <has_text_matching expression="height = 450"/> </xml> <xml name="param_counting_strategy"> |