diff hicCompartmentalization.xml @ 8:3a6a5381db36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

--- a/hicCompartmentalization.xml	Tue Jan 10 18:48:44 2023 +0000
+++ b/hicCompartmentalization.xml	Wed Oct 18 10:51:18 2023 +0000
@@ -24,17 +24,20 @@
             #end if
             --outliers $outliers
             --outputFileName plot.$image_file_format
+            #if $matrix:
+                --outputMatrix output_matrix.npz
+            #end if
         && mv plot.$image_file_format plot
 ]]>
     </command>
     <inputs>
         <expand macro="matrix_h5_cooler_multiple_macro" />
-        <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with no header. In case of several matrices with 
+        <param name="pca" type="data" format="bedgraph" label="Eigenvector file" help="A PCA vector as a bedgraph file with no header. In case of several matrices with 
                     different conditions, ie. control treatment, the PCA of control can be 
-                    used. Note that only one PCA can be provided.' />
-        <param name='quantile' type="integer" value="30" label="Quantile" help='The number of to be used quantiles.' />
-        <param name='outliers' type="float" value="0.0" label="Outliers" help='The number of outliers to be removed.' />
-        <param name="set_offset_value" type="text" optional='True' value="" label="Offset values">
+                    used. Note that only one PCA can be provided." />
+        <param name="quantile" type="integer" value="30" label="Quantile" help="The number of to be used quantiles." />
+        <param name="outliers" type="float" value="0.0" label="Outliers" help="The number of outliers to be removed." />
+        <param name="set_offset_value" type="text" optional="True" value="" label="Offset values">
             <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
         </param>
 
@@ -43,6 +46,7 @@
             <option value="svg">svg</option>
             <option value="pdf">pdf</option>
         </param>
+        <param name="matrix" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output matrix?"/>
     </inputs>
     <outputs>
         <data name="outFileName" format="png" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
@@ -51,28 +55,35 @@
                 <when input="image_file_format" value="pdf" format="pdf" />
             </change_format>
         </data>
-        <data name='output_matrix' from_work_dir='output_matrix.npz' format='binary' label='Output .npz file includes all the generated matrices'>
-            <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter>
+        <data name="output_matrix" from_work_dir="output_matrix.npz" format="npz" label="Output .npz file includes all the generated matrices">
+            <filter>matrix</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
             <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" />
             <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
             <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" />
-            <param name="quantile" value='30' />
+            <param name="quantile" value="30" />
             <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
             <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" />
-            <param name="outliers" value='1.0' />
+            <param name="outliers" value="1.0" />
             <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
         </test>
+        <test expect_num_outputs="2">
+            <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
+            <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" ftype="bedgraph" />
+            <param name="matrix" value="True" />
+            <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
+            <output name="output_matrix" file="hicCompartmentsPolarization/output_matrix.npz" ftype="npz" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[