Fix tests and requirements

galaxyproteomics · Jun 28, 2024 · 308bd65 · 308bd65
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Showing 13 changed files with 71 additions and 59 deletions.
diff --git a/tools/cardinal/classification.xml b/tools/cardinal/classification.xml
@@ -4,8 +4,8 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
+        <!--requirement type="package" version="2.3">r-gridextra</requirement>
+        <requirement type="package" version="3.3.5">r-ggplot2</requirement-->
     </expand>
     <command detect_errors="exit_code">
         <![CDATA[

diff --git a/tools/cardinal/combine.xml b/tools/cardinal/combine.xml
@@ -6,9 +6,9 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
+        <!--requirement type="package" version="3.3.5">r-ggplot2</requirement>
         <requirement type="package" version="0.12">r-maldiquantforeign</requirement>
-        <requirement type="package" version="1.20">r-maldiquant</requirement>
+        <requirement type="package" version="1.20">r-maldiquant</requirement-->
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[

diff --git a/tools/cardinal/filtering.xml b/tools/cardinal/filtering.xml
@@ -4,8 +4,8 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
+        <!--requirement type="package" version="2.3">r-gridextra</requirement>
+        <requirement type="package" version="3.3.5">r-ggplot2</requirement-->
     </expand>
     <expand macro="print_version"/>
     <command detect_errors="exit_code">

diff --git a/tools/cardinal/macros.xml b/tools/cardinal/macros.xml
@@ -6,6 +6,16 @@
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-cardinal</requirement>
             <!--requirement type="package" version="3.6.1">r-base</requirement-->
+            <requirement type="package" version="2.3">r-gridextra</requirement>
+            <requirement type="package" version="3.5.1">r-ggplot2</requirement>
+            <requirement type="package" version="0.14.1">r-maldiquantforeign</requirement>
+            <requirement type="package" version="1.22.2">r-maldiquant</requirement>
+            <requirement type="package" version="3.50.0">bioconductor-sva</requirement>
+            <requirement type="package" version="1.1.0.1">r-randomcolor</requirement>
+            <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>
+            <requirement type="package" version="2.23_24">r-kernsmooth</requirement>
+            <requirement type="package" version="1.3.0">r-scales</requirement>
+            <requirement type="package" version="1.0.12">r-pheatmap</requirement>
             <yield/>
         </requirements>
     </xml>

diff --git a/tools/cardinal/mz_images.xml b/tools/cardinal/mz_images.xml
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
+        <!--requirement type="package" version="2.3">r-gridextra</requirement-->
     </expand>
     <command detect_errors="aggressive">
 <![CDATA[

diff --git a/tools/cardinal/preprocessing.xml b/tools/cardinal/preprocessing.xml
@@ -6,10 +6,10 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
+        <!--requirement type="package" version="2.3">r-gridextra</requirement>
         <requirement type="package" version="3.4.0">r-ggplot2</requirement>
         <requirement type="package" version="3.50.0">bioconductor-sva</requirement>
-        <requirement type="package" version="1.1.0.1">r-randomcolor</requirement>
+        <requirement type="package" version="1.1.0.1">r-randomcolor</requirement-->
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[

diff --git a/tools/cardinal/quality_report.xml b/tools/cardinal/quality_report.xml
@@ -6,12 +6,12 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
+        <!--requirement type="package" version="2.3">r-gridextra</requirement>
         <requirement type="package" version="3.3.5">r-ggplot2</requirement>
         <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
         <requirement type="package" version="2.23_20">r-kernsmooth</requirement>
         <requirement type="package" version="1.1.1">r-scales</requirement>
-        <requirement type="package" version="1.0.12">r-pheatmap</requirement>
+        <requirement type="package" version="1.0.12">r-pheatmap</requirement-->
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[

diff --git a/tools/cardinal/segmentation.xml b/tools/cardinal/segmentation.xml
@@ -4,8 +4,8 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
+        <!--requirement type="package" version="2.3">r-gridextra</requirement>
+        <requirement type="package" version="3.3.5">r-ggplot2</requirement-->
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[

diff --git a/tools/cardinal/spatial_DGMM.xml b/tools/cardinal/spatial_DGMM.xml
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
+        <!--requirement type="package" version="2.3">r-gridextra</requirement-->
       </expand>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -213,55 +213,57 @@ change in log-likelihood."/>
     </outputs>
     <tests>
         <test expect_num_outputs="4">
-	    <param name="infile" value="" ftype="imzml">
-	        <composite_data value="spatial_DGMM_input.imzML"/>
-	        <composite_data value="spatial_DGMM_input.ibd"/>
-	    </param>
-	    <param name="r" value="1"/>
-	    <param name="k" value="6"/>
-	    <param name="method" value="adaptive"/>
-	    <param name="dist" value="radial"/>
-	    <param name="annealing" value="TRUE"/>
+            <param name="infile" value="" ftype="imzml">
+                <composite_data value="spatial_DGMM_input.imzML"/>
+                <composite_data value="spatial_DGMM_input.ibd"/>
+            </param>
+            <param name="r" value="1"/>
+            <param name="k" value="6"/>
+            <param name="method" value="adaptive"/>
+            <param name="dist" value="radial"/>
+            <param name="annealing" value="TRUE"/>
+            <param name="setseed" value="7353"/>
             <param name="output_estimates" value="True"/>
             <param name="output_probability" value="True"/>
-	    <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/>
-	    <output name="dgmm_summary" file="dgmm_summary1.tabular"/>
-	    <output_collection name="estimates_output" type="list" count="10">
+            <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/>
+            <output name="dgmm_summary" file="dgmm_summary1.tabular"/>
+            <output_collection name="estimates_output" type="list" count="10">
                 <element name="estimates_r1_k6_mz1135.93347167969" file="estimates_r1_k6_mz1135.93347167969.tabular"/>
             </output_collection>
             <output_collection name="probability_output" type="list" count="10">
                 <element name="probability_r1_k6_mz1023.70806884766" file="probability_r1_k6_mz1023.70806884766.tabular"/>
             </output_collection>
         </test>
         <test expect_num_outputs="6">
-        <param name="infile" value="" ftype="imzml">
-            <composite_data value="spatial_DGMM_input.imzML"/>
-            <composite_data value="spatial_DGMM_input.ibd"/>
-        </param>
-        <conditional name="sample_groups">
-            <param name="group" value="multiple_groups"/>
-            <param name="annotation_file" value="DGMM_annotations.tabular"/>
-            <param name="column_x" value="1"/>
-            <param name="column_y" value="2"/>
-            <param name="column_names" value="3"/>
-            <param name="tabular_header" value="True"/>
-        </conditional>
-        <param name="r" value="2"/>
-	    <param name="k" value="10"/>
-	    <param name="annealing" value="TRUE"/>
-        <param name="output_estimates" value="True"/>
-        <param name="output_probability" value="True"/>
-        <param name="output_plots" value="True"/>
-        <param name="output_rdata" value="True"/>
-        <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/>
-        <output name="dgmm_summary" file="dgmm_summary2.tabular"/>
-        <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/>
-        <output_collection name="estimates_output" type="list" count="10">
-            <element name="estimates_r2_k10_mz1200.46533203125" file="estimates_r2_k10_mz1200.46533203125.tabular"/>
-        </output_collection>
-        <output_collection name="probability_output" type="list" count="10">
-            <element name="probability_r2_k10_mz1135.93347167969" file="probability_r2_k10_mz1135.93347167969.tabular"/>
-        </output_collection>
+            <param name="infile" value="" ftype="imzml">
+                <composite_data value="spatial_DGMM_input.imzML"/>
+                <composite_data value="spatial_DGMM_input.ibd"/>
+            </param>
+            <conditional name="sample_groups">
+                <param name="group" value="multiple_groups"/>
+                <param name="annotation_file" value="DGMM_annotations.tabular"/>
+                <param name="column_x" value="1"/>
+                <param name="column_y" value="2"/>
+                <param name="column_names" value="3"/>
+                <param name="tabular_header" value="True"/>
+            </conditional>
+            <param name="r" value="2"/>
+            <param name="k" value="10"/>
+            <param name="annealing" value="TRUE"/>
+            <param name="setseed" value="7353"/>
+            <param name="output_estimates" value="True"/>
+            <param name="output_probability" value="True"/>
+            <param name="output_plots" value="True"/>
+            <param name="output_rdata" value="True"/>
+            <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/>
+            <output name="dgmm_summary" file="dgmm_summary2.tabular"/>
+            <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/>
+            <output_collection name="estimates_output" type="list" count="10">
+                <element name="estimates_r2_k10_mz1200.46533203125" file="estimates_r2_k10_mz1200.46533203125.tabular"/>
+            </output_collection>
+            <output_collection name="probability_output" type="list" count="10">
+                <element name="probability_r2_k10_mz1135.93347167969" file="probability_r2_k10_mz1135.93347167969.tabular"/>
+            </output_collection>
         </test>         
     </tests>
     <help>

diff --git a/tools/cardinal/spectra_plots.xml b/tools/cardinal/spectra_plots.xml
@@ -6,9 +6,9 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
+        <!--requirement type="package" version="3.3.5">r-ggplot2</requirement>
         <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="1.1.1">r-scales</requirement>
+        <requirement type="package" version="1.1.1">r-scales</requirement-->
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[

diff --git a/tools/cardinal/test-data/dgmm_test1.pdf b/tools/cardinal/test-data/dgmm_test1.pdf
diff --git a/tools/cardinal/test-data/dgmm_test2.pdf b/tools/cardinal/test-data/dgmm_test2.pdf
diff --git a/tools/cardinal/test-data/estimates_r1_k6_mz1135.93347167969.tabular b/tools/cardinal/test-data/estimates_r1_k6_mz1135.93347167969.tabular
@@ -1,4 +1,4 @@
 group	class	mean	var
-files_	1	0.224949111319976	0.133976695047921
-files_	2	5.01787928237365	0.301220362077463
-files_	3	6.64940193494161	0.752878508867188
+Composite Dataset	1	0.224949111319976	0.133976695047921
+Composite Dataset	2	5.01787928237365	0.301220362077463
+Composite Dataset	3	6.64940193494161	0.752878508867188