| Previous changeset 18:0185bd174ea0 (2024-09-19) Next changeset 20:62acdd96d4a0 (2024-10-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f |
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modified:
macros.xml plot.xml |
| b |
| diff -r 0185bd174ea0 -r 40812a65a78b macros.xml --- a/macros.xml Thu Sep 19 06:44:22 2024 +0000 +++ b/macros.xml Thu Oct 03 22:44:36 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.10.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements> @@ -10,6 +10,7 @@ <requirement type="package" version="2.2.2">pandas</requirement> <requirement type="package" version="1.14.1">scipy</requirement> <requirement type="package" version="0.14.2">statsmodels</requirement> + <requirement type="package" version="0.3.5">fa2</requirement> <yield /> </requirements> </xml> @@ -587,7 +588,7 @@ ]]> </token> <token name="@CMD_SHOW_NONE@"><![CDATA[ - show=None + show=None ]]> </token> <token name="@CMD_VAR_NAMES_HEADER_CHECK@"><![CDATA[ @@ -1197,14 +1198,13 @@ </xml> <xml name="params_pl_paga"> <param argument="threshold" type="float" min="0" value="" optional="true" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/> - <expand macro="param_groups"/> + <param argument="labels" type="text" value="" optional="true" label="The node labels" help="This defaults to the group labels stored in the categorical for which paga() has been computed"> + <expand macro="sanitize_query"/> + </param> <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'."> <expand macro="sanitize_query"/> </param> <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing"/> - <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which 'tl.paga' has been computed."> - <expand macro="sanitize_query"/> - </param> <expand macro="param_layout"/> <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout"/> <param argument="random_state" type="integer" value="0" label="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/> @@ -1237,9 +1237,9 @@ #if str($method.threshold) != '': threshold=$method.threshold, #end if - #if str($method.groups) != '': - #set $groups=([x.strip() for x in str($method.groups).split(',')]) - groups=$groups, + #if str($method.labels) != '': + #set $labels=([x.strip() for x in str($method.labels).split(',')]) + labels=$labels, #end if #if str($method.color) != '': #set $color=([x.strip() for x in str($method.color).split(',')]) @@ -1248,10 +1248,6 @@ #if $method.pos: pos=np.fromfile($method.pos, dtype=dt), #end if - #if str($method.labels) != '': - #set $labels=([x.strip() for x in str($method.labels).split(',')]) - labels=$labels, - #end if layout='$method.layout', #if $method.init_pos: init_pos=np.fromfile($method.init_pos, dtype=dt), @@ -1269,7 +1265,9 @@ dashed_edges='$method.dashed_edges', #end if single_component=$method.single_component, + #if str($method.fontsize) != '': fontsize=$method.fontsize, + #end if node_size_scale=$method.node_size_scale, node_size_power=$method.node_size_power, edge_width_scale=$method.edge_width_scale, |
| b |
| diff -r 0185bd174ea0 -r 40812a65a78b plot.xml --- a/plot.xml Thu Sep 19 06:44:22 2024 +0000 +++ b/plot.xml Thu Oct 03 22:44:36 2024 +0000 |
| [ |
| b'@@ -75,7 +75,7 @@\n legend_fontweight=\'$method.plot.legend_fontweight\',\n #if $method.plot.color_map:\n color_map=\'$method.plot.color_map\',\n- #end if \n+ #end if\n #if $method.plot.palette:\n palette=[\'$method.plot.palette\'],\n #end if\n@@ -98,7 +98,7 @@\n @CMD_VAR_NAMES_HEADER_CHECK@\n sc.pl.dotplot(\n @CMD_PARAM_PLOT_INPUTS@\n- @CMD_PARAMS_INPUTS@ \n+ @CMD_PARAMS_INPUTS@\n @CMD_PARAM_GENE_SYMBOLS@\n @CMD_PARAMS_PLOTS@\n @CMD_PL_DOTPLOT@\n@@ -259,7 +259,7 @@\n @CMD_PARAM_GROUPS@\n @CMD_PARAMS_PL_ATTRIBUTE_SECTION@\n @CMD_SCATTER_OUTINE@\n- @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@ \n+ @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@\n @CMD_SHOW_NONE@)\n \n #else if str($method.method) == \'pl.tsne\':\n@@ -274,7 +274,7 @@\n @CMD_PARAM_GROUPS@\n @CMD_PARAMS_PL_ATTRIBUTE_SECTION@\n @CMD_SCATTER_OUTINE@\n- @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@ \n+ @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@\n @CMD_PARAM_LAYER@\n @CMD_SHOW_NONE@)\n \n@@ -366,6 +366,8 @@\n @CMD_PARAMS_PL_PAGA@\n @CMD_SHOW_NONE@)\n \n+@CMD_ANNDATA_WRITE_OUTPUTS@\n+\n #else if str($method.method) == \'pl.paga_compare\':\n sc.pl.paga_compare(\n @CMD_PARAM_PLOT_INPUTS@\n@@ -379,7 +381,7 @@\n legend_fontweight=\'$method.plot.legend_fontweight\',\n #if $method.plot.color_map:\n color_map=\'$method.plot.color_map\',\n- #end if \n+ #end if\n #if $method.plot.palette:\n palette=[\'$method.plot.palette\'],\n #end if\n@@ -643,7 +645,7 @@\n <expand macro="conditional_stripplot"/>\n <conditional name="multi_panel">\n <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when \'groupby is not provided">\n- <option value="None" selected="true">No</option> \n+ <option value="None" selected="true">No</option>\n <option value="True">Yes</option>\n </param>\n <when value="None"/>\n@@ -994,6 +996,9 @@\n <data name="hidden_output" format="txt" label="Log file" hidden="true" >\n <filter>advanced_common[\'show_log\']</filter>\n </data>\n+ <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">\n+ <filter>method[\'method\'] == \'pl.paga\'</filter>\n+ </data>\n </outputs>\n <tests>\n <!-- test 1 -->\n@@ -1036,7 +1041,7 @@\n </output>\n <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 2 -->\n <test expect_num_outputs="2">\n <param name="adata" value="krumsiek11.h5ad"/>\n@@ -1076,7 +1081,7 @@\n </output>\n <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 3 -->\n <test expect_num_outputs="2">\n <param name="adata" value="pbmc68k_reduced.h5ad"/>\n@@ -1154,7 +1159,7 @@\n </output>\n <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 5 -->\n <test expect_num_outputs="2">\n <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>\n@@ -1200,7 +1205,7 @@\n </assert_contents>\n </output>\n </test>\n- \n+\n <!-- test 6 -->\n <test expect_num_outputs="2">\n <param name="adata" value="pbmc68k_reduced.h5ad"/>\n@@ -1250,7 +1255,7 @@\n </output>\n <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 7 -->\n <test expect_num_outputs="2">\n <par'..b'aul15_subsample.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 29 -->\n- <test expect_num_outputs="1">\n+ <test expect_num_outputs="2">\n <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>\n <param name="format" value="png"/>\n <conditional name="method">\n@@ -1940,8 +1945,13 @@\n <param name="edge_width_scale" value="5"/>\n </conditional>\n <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>\n+ <output name="anndata_out" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="uns/paga"/>\n+ </assert_contents>\n+ </output>\n </test>\n- \n+\n <!-- test 30 -->\n <test expect_num_outputs="1">\n <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>\n@@ -1961,14 +1971,14 @@\n <!-- <test expect_num_outputs="2">\n test pl.paga_path\n </test> -->\n- \n+\n <!-- test 32 -->\n <test expect_num_outputs="2">\n <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>\n <param name="format" value="png"/>\n <conditional name="method">\n <param name="method" value="pl.rank_genes_groups"/>\n- <param name="n_genes" value="10"/> \n+ <param name="n_genes" value="10"/>\n </conditional>\n <section name="advanced_common">\n <param name="show_log" value="true"/>\n@@ -1983,7 +1993,7 @@\n </output>\n <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 33 -->\n <test expect_num_outputs="2">\n <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>\n@@ -2018,7 +2028,7 @@\n <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/>\n </output_collection>\n </test>\n- \n+\n <!-- test 34 -->\n <test expect_num_outputs="2">\n <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>\n@@ -2056,7 +2066,7 @@\n </output>\n <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/>\n </test>\n- \n+\n <!-- test 35 -->\n <test expect_num_outputs="2">\n <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>\n@@ -2105,7 +2115,7 @@\n </output>\n <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 37 -->\n <test expect_num_outputs="2">\n <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>\n@@ -2130,7 +2140,7 @@\n </output>\n <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 38 pl.rank_genes_groups_dotplot with marker list-->\n <test expect_num_outputs="2">\n <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />\n@@ -2155,7 +2165,7 @@\n </output>\n <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/>\n </test>\n- \n+\n <!-- test 39: pl.rank_genes_groups_dotplot with marker list -->\n <test expect_num_outputs="2">\n <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />\n' |