Mercurial > repos > galaxyp > cardinal_single_ion_segmentation

diff spatial_DGMM.xml @ 2:fd6c9bc77405 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author galaxyp
date Thu, 04 Jul 2024 13:28:45 +0000
parents 75b43378fb02
children
line wrap: on
line diff
--- a/spatial_DGMM.xml	Wed Apr 19 22:22:32 2023 +0000
+++ b/spatial_DGMM.xml	Thu Jul 04 13:28:45 2024 +0000
@@ -1,11 +1,9 @@
-<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@VERSION@.0">
+<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>mass spectrometry imaging spatial DGMM</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
-      </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
 
@@ -66,7 +64,6 @@
         
     ## set seed to make analysis reproducible
     set.seed($setseed)
-    
 
     ## single ion segmentation
     dgmm <- spatialDGMM(msidata, 
@@ -156,7 +153,7 @@
                     <expand macro="reading_pixel_annotations"/>
                 </when>
             </conditional>
-	    <param name="r" type="text" value="2"
+	        <param name="r" type="text" value="2"
                    label="r" help="The spatial neighborhood radius of nearby pixels to consider. Only a single value is allowed">
                    <expand macro="sanitizer_multiple_digits"/>
             </param>
@@ -213,56 +210,82 @@
         </collection>
     </outputs>
     <tests>
-        <test>
-	    <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"/>
+        <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="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">
-                <element name="estimates_r1_k6_mz1135.93347167969" file="estimates_r1_k6_mz1135.93347167969.tabular"/>
+            <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">
+                    <assert_contents>
+                        <has_text text="files_"/>
+                        <has_text text="3"/>
+                        <has_text_matching expression="0\.\d+"/>
+                    </assert_contents>
+                </element>
             </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"/>
+                <element name="probability_r1_k6_mz1023.70806884766">
+                    <assert_contents>
+                        <has_text text="xy_16_1"/>
+                        <has_text text="3"/>
+                        <has_text_matching expression="0\.\d+"/>
+                    </assert_contents>
+                </element>
             </output_collection>
         </test>
-        <test>
-        <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>
+        <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="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">
+                    <assert_contents>
+                        <has_text text="circle"/>
+                        <has_text text="3"/>
+                        <has_text_matching expression="0\.\d+"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="probability_output" type="list" count="10">
+                <element name="probability_r2_k10_mz1135.93347167969">
+                    <assert_contents>
+                        <has_text text="xy_9_1"/>
+                        <has_text text="3"/>
+                        <has_text_matching expression="0\.\d+"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>         
     </tests>
     <help>