Repository 'scanpy_filter'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter

Changeset 3:0a6de5e65992 (2019-12-12)
Previous changeset 2:e62673c32a5d (2019-12-05) Next changeset 4:a72e9faea895 (2019-12-18)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
modified:
filter.xml
macros.xml
test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad
added:
test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png
test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png
test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png
test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png
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diff -r e62673c32a5d -r 0a6de5e65992 filter.xml
--- a/filter.xml Thu Dec 05 07:14:15 2019 -0500
+++ b/filter.xml Thu Dec 12 09:28:18 2019 -0500
b
@@ -113,12 +113,12 @@
         <expand macro="inputs_anndata"/>
         <conditional name="method">
             <param argument="method" type="select" label="Method used for filtering">
-                <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`</option>
-                <option value="pp.filter_genes">Filter genes based on number of cells or counts, using `pp.filter_genes`</option>
-                <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using `tl.filter_rank_genes_groups`</option>
-                <option value="pp.highly_variable_genes">, using `tl.highly_variable_genes`</option>
-                <option value="pp.subsample">Subsample to a fraction of the number of observations, using `pp.subsample`</option>
-                <option value="pp.downsample_counts">Downsample counts from count matrix, using `pp.downsample_counts`</option>
+                <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option>
+                <option value="pp.filter_genes">Filter genes based on number of cells or counts, using 'pp.filter_genes'</option>
+                <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using 'tl.filter_rank_genes_groups'</option>
+                <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using 'pp.highly_variable_genes'</option>
+                <option value="pp.subsample">Subsample to a fraction of the number of observations, using 'pp.subsample'</option>
+                <option value="pp.downsample_counts">Downsample counts from count matrix, using 'pp.downsample_counts'</option>
             </param>
             <when value="pp.filter_cells">
                 <conditional name="filter">
@@ -177,8 +177,8 @@
             <when value="pp.highly_variable_genes">
                 <conditional name='flavor'>
                     <param argument="flavor" type="select" label="Flavor for computing normalized dispersion">
-                        <option value="seurat">seurat: expects non-logarithmized data</option>
-                        <option value="cell_ranger">cell_ranger: usually called for logarithmized data</option>
+                        <option value="seurat">Seurat</option>
+                        <option value="cell_ranger">Cell Ranger</option>
                     </param>
                     <when value="seurat">
                         <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff"/>
@@ -191,7 +191,7 @@
                     </when>
                 </conditional>
                 <param argument="n_bins" type="integer" value="20" label="Number of bins for binning the mean gene expression" help="Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1"/>
-                <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/>
+                <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/>
             </when>
             <when value="pp.subsample">
                 <conditional name="type">
@@ -200,7 +200,7 @@
                         <option value="n_obs">By number of observation</option>
                     </param>
                     <when value="fraction">
-                        <param argument="fraction" type="float" value="" label="Subsample to this `fraction` of the number of observations"/>
+                        <param argument="fraction" type="float" value="" label="Subsample to this 'fraction' of the number of observations"/>
                     </when>
                     <when value="n_obs">
                         <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations"/>
@@ -329,12 +329,14 @@
                     <param name="n_top_genes" value="2"/>
                 </conditional>
                 <param name="n_bins" value="20"/>
+                <param name="subset" value="true"/>
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="sc.pp.highly_variable_genes"/>
                 <has_text_matching expression="flavor='cell_ranger'"/>
                 <has_text_matching expression="n_top_genes=2"/>
                 <has_text_matching expression="n_bins=20"/>
+                <has_text_matching expression="subset=True"/>
             </assert_stdout>
             <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
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diff -r e62673c32a5d -r 0a6de5e65992 macros.xml
--- a/macros.xml Thu Dec 05 07:14:15 2019 -0500
+++ b/macros.xml Thu Dec 12 09:28:18 2019 -0500
[
b'@@ -1,7 +1,7 @@\n <macros>\n     <token name="@version@">1.4.4.post1</token>\n     <token name="@profile@">19.01</token>\n-    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>\n+    <token name="@galaxy_version@"><![CDATA[@version@+galaxy1]]></token>\n     <xml name="requirements">\n         <requirements>\n             <requirement type="package" version="@version@">scanpy</requirement>\n@@ -351,10 +351,10 @@\n         <option value="gist_ncar">gist_ncar (Miscellaneous)</option>\n     </xml>\n     <xml name="param_groupby">\n-        <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the heatmap is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into `num_categories`."/>\n+        <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the plot is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into \'num_categories\'."/>\n     </xml>\n     <xml name="param_use_raw">\n-        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/>\n+        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use \'raw\' attribute of input if present" help=""/>\n     </xml>\n     <xml name="param_log">\n         <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/>\n@@ -378,12 +378,12 @@\n     <xml name="pl_var_names">\n         <conditional name="var_names">\n             <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >\n-                <option value="all">All variables in `adata.var_names`</option>\n-                <option value="custom">Subset of variables in `adata.var_names`</option>\n+                <option value="all">All variables in \'adata.var_names\'</option>\n+                <option value="custom">Subset of variables in \'adata.var_names\'</option>\n             </param>\n             <when value="all"/>\n             <when value="custom">\n-                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of `adata.var_names`, and separated by comma"/>\n+                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of \'adata.var_names\', and separated by comma"/>\n             </when>\n         </conditional>\n     </xml>\n@@ -404,27 +404,20 @@\n         <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/>\n     </xml>\n     <xml name="param_layer">\n-        <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default `adata.raw.X` is plotted. If `use_raw=False` is set, then `adata.X` is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over `use_raw`."/>\n+        <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default \'adata.raw.X\' is plotted. If \'use_raw=False\' is set, then \'adata.X\' is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over \'use_raw\'."/>\n     </xml>\n     <token name="@CMD_param_plot_inputs@"><![CDATA[\n     adata,\n     save=\'.$format\',\n     show=False,\n     ]]></token>\n-    <xml name="params_plots">\n+    <xml name="params_inputs">\n         <expand macro="pl_var_names"/>\n         <expand macro="param_groupby"/>\n-        <expand macro="param_log"/>'..b'_pl_heatmap@"><![CDATA[\n+    swap_axes=$method.swap_axes,\n+    show_gene_labels=$method.show_gene_labels,\n+    cmap=\'$method.matplotlib_pyplot_imshow.cmap\',\n+    #if str($method.matplotlib_pyplot_imshow.interpolation) != \'None\'\n+    interpolation=\'$method.matplotlib_pyplot_imshow.interpolation\',\n+    #end if\n+    #if $method.matplotlib_pyplot_imshow.alpha\n+    alpha=$method.matplotlib_pyplot_imshow.alpha,\n+    #end if\n+    #if $method.matplotlib_pyplot_imshow.vmin\n+    vmin=$method.matplotlib_pyplot_imshow.vmin,\n+    #end if\n+    #if $method.matplotlib_pyplot_imshow.vmax\n+    vmax=$method.matplotlib_pyplot_imshow.vmax,\n+    #end if\n+    origin=\'$method.matplotlib_pyplot_imshow.origin\'\n+    ]]>\n+    </token>\n+    <xml name="pl_rank_genes_groups_ext">\n+        <expand macro="param_groups"/>\n+        <expand macro="param_n_genes"/>\n+        <expand macro="param_key"/>\n+    </xml>\n+    <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[\n+    @CMD_params_groups@\n+    #if str($method.n_genes) != \'\'\n+    n_genes=$method.n_genes,\n+    #end if\n+    #if str($method.key) != \'\'\n+    key=\'$method.key\',\n+    #end if\n+    ]]>\n+    </token>\n+    <xml name="pl_matrixplot">\n+        <expand macro="param_swap_axes"/>\n+        <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">\n+            <param argument="cmap" type="select" label="Color palette">\n+                <expand macro="seaborn_color_palette_options"/>\n+            </param>\n+            <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>\n+            <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>\n+            <expand macro="param_matplotlib_pyplot_edgecolors"/>\n+            <expand macro="param_alpha"/>\n+            <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>\n+        </section>\n+    </xml>\n+    <token name="@CMD_pl_matrixplot@"><![CDATA[\n+    swap_axes=$method.swap_axes,\n+    cmap=\'$method.matplotlib_pyplot_pcolor.cmap\',\n+    #if $method.matplotlib_pyplot_pcolor.vmin\n+    vmin=$method.matplotlib_pyplot_pcolor.vmin,\n+    #end if\n+    #if $method.matplotlib_pyplot_pcolor.vmax\n+    vmax=$method.matplotlib_pyplot_pcolor.vmax,\n+    #end if\n+    edgecolors=\'$method.matplotlib_pyplot_pcolor.edgecolors\',\n+    #if $method.matplotlib_pyplot_pcolor.alpha\n+    alpha=$method.matplotlib_pyplot_pcolor.alpha,\n+    #end if\n+    snap=$method.matplotlib_pyplot_pcolor.snap\n+    ]]>\n+    </token>\n+    <xml name="pl_stacked_violin">\n+        <expand macro="param_swap_axes"/>\n+        <section name="violin_plot" title="Violin plot attributes">\n+            <expand macro="conditional_stripplot"/>\n+            <expand macro="param_scale"/>\n+        </section>\n+        <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">\n+            <option value="muted">muted</option>\n+            <expand macro="seaborn_color_palette_options"/>\n+        </param>\n+        <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">\n+            <option value="None">No standardization</option>\n+            <option value="var">Standardization on variable</option>\n+            <option value="obs">Standardization on observation</option>\n+        </param>\n+        <expand macro="seaborn_violinplot"/>\n+    </xml>\n+    <token name="@CMD_pl_stacked_violin@"><![CDATA[\n+    swap_axes=$method.swap_axes,\n+    @CMD_conditional_stripplot@\n+    scale=\'$method.violin_plot.scale\',\n+    row_palette=\'$method.row_palette\',\n+    #if str($method.standard_scale) != \'None\'\n+    standard_scale=\'$method.standard_scale\',\n+    #end if\n+    @CMD_params_seaborn_violinplot@\n+    ]]>\n+    </token>\n </macros>\n'
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diff -r e62673c32a5d -r 0a6de5e65992 test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png
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diff -r e62673c32a5d -r 0a6de5e65992 test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png
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diff -r e62673c32a5d -r 0a6de5e65992 test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png
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diff -r e62673c32a5d -r 0a6de5e65992 test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad
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