Mercurial > repos > iuc > scanpy_plot

diff plot.xml @ 9:9a169729c9f9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
author iuc
date Mon, 12 Apr 2021 18:15:46 +0000
parents 6adf98e782f3
children aa0c474463c2
line wrap: on
line diff
--- a/plot.xml	Tue Mar 16 13:01:04 2021 +0000
+++ b/plot.xml	Mon Apr 12 18:15:46 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_plot" name="Plot" version="1.7.1+galaxy1" profile="@profile@">
     <description> with scanpy</description>
     <macros>
         <import>macros.xml</import>
@@ -59,6 +59,9 @@
 #else if $method.method == 'pl.heatmap'
 sc.pl.heatmap(
     @CMD_param_plot_inputs@
+    #if str($method.gene_symbols) != ''
+    gene_symbols='$method.gene_symbols',
+    #end if
     @CMD_params_inputs@
     @CMD_params_plots@
     @CMD_pl_heatmap@)
@@ -66,6 +69,9 @@
 #else if $method.method == 'pl.dotplot'
 sc.pl.dotplot(
     @CMD_param_plot_inputs@
+    #if str($method.gene_symbols) != ''
+    gene_symbols='$method.gene_symbols',
+    #end if
     @CMD_params_inputs@
     @CMD_params_plots@
     @CMD_pl_dotplot@)
@@ -103,6 +109,9 @@
 #else if $method.method == 'pl.stacked_violin'
 sc.pl.stacked_violin(
     @CMD_param_plot_inputs@
+    #if str($method.gene_symbols) != ''
+    gene_symbols='$method.gene_symbols',
+    #end if
     @CMD_params_inputs@
     @CMD_params_plots@
     @CMD_pl_stacked_violin@)
@@ -110,6 +119,9 @@
 #else if $method.method == 'pl.matrixplot'
 sc.pl.matrixplot(
     @CMD_param_plot_inputs@
+    #if str($method.gene_symbols) != ''
+    gene_symbols='$method.gene_symbols',
+    #end if
     @CMD_params_inputs@
     @CMD_params_plots@
     @CMD_pl_matrixplot@)
@@ -474,11 +486,13 @@
             </when>
             <when value="pl.heatmap">
                 <expand macro="params_inputs"/>
+                <expand macro="gene_symbols"/>
                 <expand macro="params_plots"/>
                 <expand macro="pl_heatmap"/>
             </when>
             <when value="pl.dotplot">
                 <expand macro="params_inputs"/>
+                <expand macro="gene_symbols"/>
                 <expand macro="params_plots"/>
                 <expand macro="pl_dotplot"/>
             </when>
@@ -523,11 +537,13 @@
             </when>
             <when value="pl.stacked_violin">
                 <expand macro="params_inputs"/>
+                <expand macro="gene_symbols"/>
                 <expand macro="params_plots"/>
                 <expand macro="pl_stacked_violin"/>
             </when>
             <when value="pl.matrixplot">
                 <expand macro="params_inputs"/>
+                <expand macro="gene_symbols"/>
                 <expand macro="params_plots"/>
                 <expand macro="pl_matrixplot"/>
             </when>
@@ -917,6 +933,56 @@
             <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
+          <!-- test 2.1: pl.heatmap with symbols !-->
+          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
+          <param name="format" value="png"/>
+          <conditional name="method">
+              <param name="method" value="pl.heatmap"/>
+              <conditional name="var_names">
+                  <param name="type" value="custom"/>
+                  <param name="var_names" value="Fog1,EKLF,SCL"/>
+              </conditional>
+              <param name="groupby" value="cell_type"/>
+              <param name="gene_symbols" value="symbol"/>
+              <param name="num_categories" value="7"/>
+              <param name="log" value="False"/>
+              <param name="use_raw" value="False"/>
+              <conditional name="figsize">
+                  <param name="test" value="yes"/>
+                  <param name="width" value="10" />
+                  <param name="height" value="3"/>
+              </conditional>
+              <param name="dendrogram" value="True"/>
+              <param name="swap_axes" value="True"/>
+              <param name="show_gene_labels" value="True"/>
+              <section name="matplotlib_pyplot_imshow">
+                  <param name="cmap" value="YlGnBu"/>
+                  <param name="interpolation" value="None"/>
+                  <param name="origin" value="upper"/>
+              </section>
+          </conditional>
+          <section name="advanced_common">
+              <param name="show_log" value="true" />
+          </section>
+          <output name="hidden_output">
+              <assert_contents>
+                  <has_text_matching expression="sc.pl.heatmap"/>
+                  <has_text_matching expression="gene_symbols='symbol'"/>
+                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
+                  <has_text_matching expression="groupby='cell_type'"/>
+                  <has_text_matching expression="log=False"/>
+                  <has_text_matching expression="use_raw=False"/>
+                  <has_text_matching expression="num_categories=7"/>
+                  <has_text_matching expression="dendrogram=True"/>
+                  <has_text_matching expression="figsize=\(10, 3\)"/>
+                  <has_text_matching expression="swap_axes=True"/>
+                  <has_text_matching expression="show_gene_labels=True"/>
+                  <has_text_matching expression="cmap='YlGnBu'"/>
+                  <has_text_matching expression="origin='upper'"/>
+              </assert_contents>
+          </output>
+        </test>
+        <test>
             <!-- test 3: pl.dotplot !-->
             <param name="adata" value="pbmc68k_reduced.h5ad" />
             <param name="format" value="png"/>
@@ -976,6 +1042,44 @@
             <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
+          <!-- test 3.1: pl.dotplot with symbols !-->
+          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
+          <param name="format" value="png"/>
+          <conditional name="method">
+              <param name="method" value="pl.dotplot"/>
+              <conditional name="var_names">
+                  <param name="type" value="custom"/>
+                  <param name="var_names" value="Fog1,EKLF,SCL"/>
+              </conditional>
+              <param name="groupby" value="cell_type"/>
+              <param name="gene_symbols" value="symbol"/>
+              <param name="num_categories" value="7"/>
+              <param name="log" value="False"/>
+              <param name="use_raw" value="False"/>
+              <param name="dendrogram" value="True"/>
+              <section name="matplotlib_pyplot_imshow">
+                  <param name="cmap" value="YlGnBu"/>
+                  <param name="interpolation" value="None"/>
+                  <param name="origin" value="upper"/>
+              </section>
+          </conditional>
+          <section name="advanced_common">
+              <param name="show_log" value="true" />
+          </section>
+          <output name="hidden_output">
+              <assert_contents>
+                  <has_text_matching expression="sc.pl.dotplot"/>
+                  <has_text_matching expression="gene_symbols='symbol'"/>
+                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
+                  <has_text_matching expression="groupby='cell_type'"/>
+                  <has_text_matching expression="log=False"/>
+                  <has_text_matching expression="use_raw=False"/>
+                  <has_text_matching expression="num_categories=7"/>
+                  <has_text_matching expression="dendrogram=True"/>
+              </assert_contents>
+          </output>
+        </test>
+        <test>
             <!-- test 4: pl.violin !-->
             <param name="adata" value="pbmc68k_reduced.h5ad" />
             <param name="format" value="png"/>
@@ -1093,6 +1197,41 @@
             <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
+          <!-- test 5.1: pl.stacked_violin with symbols !-->
+          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
+          <param name="format" value="png"/>
+          <conditional name="method">
+              <param name="method" value="pl.stacked_violin"/>
+              <conditional name="var_names">
+                  <param name="type" value="custom"/>
+                  <param name="var_names" value="Fog1,EKLF,SCL"/>
+              </conditional>
+              <param name="groupby" value="cell_type"/>
+              <param name="gene_symbols" value="symbol"/>
+              <param name="num_categories" value="7"/>
+              <param name="log" value="False"/>
+              <param name="use_raw" value="False"/>
+              <param name="dendrogram" value="True"/>
+              <param name="swap_axes" 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.pl.stacked_violin"/>
+                  <has_text_matching expression="gene_symbols='symbol'"/>
+                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
+                  <has_text_matching expression="groupby='cell_type'"/>
+                  <has_text_matching expression="log=False"/>
+                  <has_text_matching expression="use_raw=False"/>
+                  <has_text_matching expression="num_categories=7"/>
+                  <has_text_matching expression="dendrogram=True"/>
+                  <has_text_matching expression="swap_axes=True"/>
+              </assert_contents>
+          </output>
+        </test>
+        <test>
             <!-- test 6: pl.matrixplot !-->
             <param name="adata" value="krumsiek11.h5ad" />
             <param name="format" value="png"/>
@@ -1137,6 +1276,46 @@
             <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
+          <!-- test 6.1: pl.matrixplot with symbols !-->
+          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
+          <param name="format" value="png"/>
+          <conditional name="method">
+              <param name="method" value="pl.matrixplot"/>
+              <conditional name="var_names">
+                  <param name="type" value="custom"/>
+                  <param name="var_names" value="Fog1,EKLF,SCL"/>
+              </conditional>
+              <param name="groupby" value="cell_type"/>
+              <param name="gene_symbols" value="symbol"/>
+              <param name="num_categories" value="7"/>
+              <param name="log" value="False"/>
+              <param name="use_raw" value="False"/>
+              <conditional name="figsize">
+                  <param name="test" value="yes"/>
+                  <param name="width" value="10" />
+                  <param name="height" value="3"/>
+              </conditional>
+              <param name="dendrogram" value="True"/>
+              <param name="swap_axes" value="False"/>
+          </conditional>
+          <section name="advanced_common">
+              <param name="show_log" value="true" />
+          </section>
+          <output name="hidden_output">
+              <assert_contents>
+                  <has_text_matching expression="sc.pl.matrixplot"/>
+                  <has_text_matching expression="gene_symbols='symbol'"/>
+                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
+                  <has_text_matching expression="groupby='cell_type'"/>
+                  <has_text_matching expression="log=False"/>
+                  <has_text_matching expression="use_raw=False"/>
+                  <has_text_matching expression="num_categories=7"/>
+                  <has_text_matching expression="dendrogram=True"/>
+                  <has_text_matching expression="swap_axes=False"/>
+              </assert_contents>
+          </output>
+        </test>
+        <test>
             <!-- test 7: pl.clustermap !-->
             <param name="adata" value="krumsiek11.h5ad" />
             <param name="format" value="png"/>