add non-parametric tests

galaxyproject · Jan 11, 2025 · e0900ec · e0900ec
1 parent 08d140f
commit e0900ec
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Showing 6 changed files with 60 additions and 10 deletions.
diff --git a/tools/spacexr/macros.xml b/tools/spacexr/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.2.1=r43hdfd78af_0</token>
+    <token name="@TOOL_VERSION@">2.2.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">

diff --git a/tools/spacexr/spacexr_cside.xml b/tools/spacexr/spacexr_cside.xml
@@ -4,16 +4,15 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="edam"/>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="3.5.1">r-ggplot2</requirement>
+    </expand>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p 'inputs' 'results' 'logs' 'figures' &&
         ln -s '$rctd' 'inputs/rctd.rds' &&
         touch 'results/cside_script.R' &&
         cat '$cside_script' > 'results/cside_script.R' &&
         Rscript '$cside_script'
-        #if 'plots' in $output_selector:
-            mv 'results/de_plots/*.pdf' 'results/de_plots_quant/*.pdf' 'results/de_plots_two_regions/*.pdf' 'figures'
-        #end if
     ]]></command>
     <configfiles>
         <configfile name="cside_script"><![CDATA[
@@ -127,6 +126,7 @@ for (cell_type in cell_types) {
 
 # create plots
 #if 'plots' in $output_selector:
+library('ggplot2')
 make_all_de_plots(myRCTD, "figures")
 #end if
 # save rds file
@@ -186,7 +186,15 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.tabular$" format="tabular" directory="results"/>
         </collection>
         <collection name="de_plots" type="list" label="${tool.name} on ${on_string}: DE plots">
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" format="pdf" directory="figures"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" format="pdf" directory="figures/de_plots"/>
+            <filter>output['output_selector'] and 'plots' in output['output_selector']</filter>
+        </collection>
+        <collection name="de_plots_quant" type="list" label="${tool.name} on ${on_string}: DE plots (quant)">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" format="pdf" directory="figures/de_plots_quant"/>
+            <filter>output['output_selector'] and 'plots' in output['output_selector']</filter>
+        </collection>
+        <collection name="de_plots_two_regions" type="list" label="${tool.name} on ${on_string}: DE plots (two regions)">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" format="pdf" directory="figures/de_plots_two_regions"/>
             <filter>output['output_selector'] and 'plots' in output['output_selector']</filter>
         </collection>
         <data name="out_rds" format="rds" from_work_dir="results/cside_results.rds" label="${tool.name} on ${on_string}: RDS file">
@@ -197,6 +205,7 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
         </data>
     </outputs>
     <tests>
+        <!-- test non_parametric -->
         <test expect_num_outputs="2">
             <param name="rctd" value="myRCTD_merfish.rds"/>
             <param name="de_type" value="non_parametric"/>
@@ -206,17 +215,58 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
             <param name="fdr" value="0.25"/>
             <param name="output_selector" value="rscript" />
             <output_collection name="de_results" type="list">
-                <element name="type8" ftype="tabular">
+                <element name="Astrocytes" ftype="tabular">
+                    <assert_contents>
+                        <has_text_matching expression="Z_score.*log_fc.*se.*paramindex_best.*conv.*p_val"/>
+                        <has_text_matching expression="Gad1.*3.83906924067553.*-3.69433997573756.*0.962300949562319.*6.*TRUE.*0.00172902241856182"/>
+                    </assert_contents>
+                </element>
+                <element name="Astrocytes_sig" ftype="tabular">
+                    <assert_contents>
+                        <has_text_matching expression="Z_score.*log_fc.*se.*paramindex_best.*conv.*p_val"/>
+                        <has_text_matching expression="Glra3.*3.92715715940966.*-7.29911426576817.*1.85862545589222.*8.*TRUE.*0.00120338145955865"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="out_rscript">
+                <assert_contents>
+                    <has_text_matching expression="run.CSIDE.nonparam"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test fig and rds -->
+        <test expect_num_outputs="6">
+            <param name="rctd" value="myRCTD_merfish.rds"/>
+            <param name="de_type" value="non_parametric"/>
+            <param name="cell_types" value="Astrocytes"/>
+            <param name="cell_type_threshold" value="10"/>
+            <param name="gene_threshold" value="0.001"/>
+            <param name="fdr" value="0.25"/>
+            <param name="output_selector" value="rds,rscript,plots" />
+            <output_collection name="de_results" type="list">
+                <element name="Astrocytes" ftype="tabular">
                     <assert_contents>
-                        <has_text_matching expression="Hello"/>
+                        <has_text_matching expression="Z_score.*log_fc.*se.*paramindex_best.*conv.*p_val"/>
+                        <has_text_matching expression="Gad1.*3.83906924067553.*-3.69433997573756.*0.962300949562319.*6.*TRUE.*0.00172902241856182"/>
                     </assert_contents>
                 </element>
-                <element name="type8_sig" ftype="tabular">
+                <element name="Astrocytes_sig" ftype="tabular">
                     <assert_contents>
-                        <has_text_matching expression="Hello"/>
+                        <has_text_matching expression="Z_score.*log_fc.*se.*paramindex_best.*conv.*p_val"/>
+                        <has_text_matching expression="Glra3.*3.92715715940966.*-7.29911426576817.*1.85862545589222.*8.*TRUE.*0.00120338145955865"/>
                     </assert_contents>
                 </element>
             </output_collection>
+            <output_collection name="de_plots" type="list">
+                <element name="de_genes_Astrocytes" file="de_genes_Astrocytes.pdf" ftype="pdf" compare="sim_size"/>
+            </output_collection>
+            <output_collection name="de_plots_quant" type="list">
+                <element name="de_genes_Astrocytes" file="de_genes_Astrocytes_quant.pdf" ftype="pdf" compare="sim_size"/>
+            </output_collection>
+            <output_collection name="de_plots_two_regions" type="list">
+                <element name="de_genes_Astrocytes" file="de_genes_Astrocytes_two_regions" ftype="pdf" compare="sim_size"/>
+            </output_collection>
+            <output name="out_rds" file="cside.rds" ftype="rds" compare="sim_size"/>
             <output name="out_rscript">
                 <assert_contents>
                     <has_text_matching expression="run.CSIDE.nonparam"/>

diff --git a/tools/spacexr/test-data/cside.rds b/tools/spacexr/test-data/cside.rds
diff --git a/tools/spacexr/test-data/de_genes_Astrocytes.pdf b/tools/spacexr/test-data/de_genes_Astrocytes.pdf
diff --git a/tools/spacexr/test-data/de_genes_Astrocytes_quant.pdf b/tools/spacexr/test-data/de_genes_Astrocytes_quant.pdf
diff --git a/tools/spacexr/test-data/de_genes_Astrocytes_two_regions b/tools/spacexr/test-data/de_genes_Astrocytes_two_regions