diff hicCorrectMatrix.xml @ 21:ea19190ce5e0 draft default tip

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

--- a/hicCorrectMatrix.xml	Tue Jan 10 18:37:39 2023 +0000
+++ b/hicCorrectMatrix.xml	Wed Oct 18 10:20:07 2023 +0000
@@ -60,7 +60,7 @@
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <expand macro="matrix_h5_cooler_macro" />
         <conditional name="mode">
             <param name="mode_selector" type="select" label="Mode">
                 <option value="diagnostic_plot">Diagnostic plot</option>
@@ -71,13 +71,13 @@
                 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
             </when>
             <when value="correct">
-                <conditional name='correctionMethod'>
-                    <param name='correctionMethod_selector' type='select' label='Correction method'>
-                        <option value='ice'>Iterative_correction (Imakaev)</option>
-                        <option value='kr'>Knights-Ruiz</option>
+                <conditional name="correctionMethod">
+                    <param name="correctionMethod_selector" type="select" label="Correction method">
+                        <option value="ice">Iterative_correction (Imakaev)</option>
+                        <option value="kr">Knights-Ruiz</option>
                     </param>
 
-                    <when value='ice'>
+                    <when value="ice">
                         <param argument="--iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
 
                         <param argument="--inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
@@ -93,7 +93,7 @@
                         <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
                         <expand macro="filterThreshold" />
                     </when>
-                    <when value='kr'>
+                    <when value="kr">
                     </when>
                 </conditional>
             </when>
@@ -101,7 +101,7 @@
 
         <repeat name="chromosomes" min="0" title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
                     The order of the given chromosomes will be kept for the resulting corrected matrix">
-            <param name="chromosome" type="text" value="" label='chromosome (one per field)'>
+            <param name="chromosome" type="text" value="" label="chromosome (one per field)">
                 <validator type="empty_field" />
             </param>
         </repeat>
@@ -119,64 +119,64 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <param name="mode_selector" value="correct" />
-            <param name='correctionMethod_selector' value='ice' />
+            <param name="correctionMethod_selector" value="ice" />
             <repeat name="chromosomes">
                 <param name="chromosome" value="chrUextra" />
             </repeat>
             <repeat name="chromosomes">
                 <param name="chromosome" value="chr3LHet" />
             </repeat>
-            <param name='filterThreshold_low' value='-2.0' />
-            <param name='filterThreshold_large' value='4' />
+            <param name="filterThreshold_low" value="-2.0" />
+            <param name="filterThreshold_large" value="4" />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' />
+                    <has_h5_keys keys="correction_factors,intervals,matrix,nan_bins" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <param name="mode_selector" value="correct" />
-            <param name='correctionMethod_selector' value='kr' />
+            <param name="correctionMethod_selector" value="kr" />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='correction_factors,intervals,matrix' />
+                    <has_h5_keys keys="correction_factors,intervals,matrix" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
             <param name="mode_selector" value="correct" />
-            <param name='correctionMethod_selector' value='kr' />
+            <param name="correctionMethod_selector" value="kr" />
             <output name="outFileName" ftype="cool">
                 <assert_contents>
-                    <has_h5_keys keys='bins,chroms,indexes,pixels' />
+                    <has_h5_keys keys="bins,chroms,indexes,pixels" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
 
             <param name="mode_selector" value="correct" />
-            <param name='correctionMethod_selector' value='ice' />
+            <param name="correctionMethod_selector" value="ice" />
             <repeat name="chromosomes">
                 <param name="chromosome" value="chrUextra" />
             </repeat>
             <repeat name="chromosomes">
                 <param name="chromosome" value="chr3LHet" />
             </repeat>
-            <param name='filterThreshold_low' value='-2.0' />
-            <param name='filterThreshold_large' value='4' />
+            <param name="filterThreshold_low" value="-2.0" />
+            <param name="filterThreshold_large" value="4" />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' />
+                    <has_h5_keys keys="correction_factors,intervals,matrix,nan_bins" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <param name="mode_selector" value="diagnostic_plot" />
             <repeat name="chromosomes">