--- a/chicQualityControl.xml	Tue Jan 10 19:10:45 2023 +0000
+++ b/chicQualityControl.xml	Wed Oct 18 10:54:38 2023 +0000
@@ -28,26 +28,24 @@
     ]]>    </command>
     <inputs>
         <expand macro="matrix_h5_cooler_multiple_macro" />
-        <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
-        <param argument="--sparsity" type="float" value="0.05" label="Sparsity threshold" help='Viewpoints with a sparsity less than given are considered of bad quality. If multiple matrices are given, the viewpoint is removed as soon as it is of bad quality in at least one matrix.' />
-        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' />
+        <param argument="--referencePoints" type="data" format="interval" label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
+        <param argument="--sparsity" type="float" value="0.05" label="Sparsity threshold" help="Viewpoints with a sparsity less than given are considered of bad quality. If multiple matrices are given, the viewpoint is removed as soon as it is of bad quality in at least one matrix." />
+        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." />
 
-        <param name='dpi' type='integer' value='300' min="100" max="2000" optional='true' label='DPI for image' help='Change the default resolution of the plot.' />
+        <param name="dpi" type="integer" value="300" min="100" max="2000" optional="true" label="DPI for image" help="Change the default resolution of the plot." />
         <param name="image_file_format" type="select" label="Image output format">
             <option value="png" selected="True">png</option>
             <option value="svg">svg</option>
             <option value="pdf">pdf</option>
         </param>
+    </inputs>
 
-    </inputs>
     <outputs>
         <data name="raw_reference_points" from_work_dir="reference_points_raw_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points raw" />
         <data name="rejected_reference_points" from_work_dir="reference_points_rejected_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points rejected" />
         <data name="accepted_reference_points" from_work_dir="reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points accepted" />
         <data name="failed_reference_points" from_work_dir="reference_points_failed_reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points failed" />
-
         <data name="report" from_work_dir="reference_points_report" format="txt" label="${tool.name} on [${on_string}]: Report" />
-
         <data name="plot_histrogram" from_work_dir="histogram" format="png" label="${tool.name} on [${on_string}]: Histrogram plot">
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
@@ -61,21 +59,19 @@
             </change_format>
         </data>
     </outputs>
+
     <tests>
         <test>
             <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
             <param name="referencePoints" value="cHi-C/referencePoints.bed" />
-            <param name='sparsity' value='0.05' />
-
+            <param name="sparsity" value="0.05" />
             <output name="accepted_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed" ftype="interval" />
             <output name="raw_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter" ftype="interval" />
             <output name="rejected_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter" ftype="interval" />
             <output name="failed_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_failed_reference_points" ftype="interval" />
             <output name="report" file="cHi-C/chicQualityControl/new_referencepoints.bed_report" ftype="txt" />
-
-            <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare='sim_size' />
+            <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare="sim_size" />
             <output name="plot_sparsity" file="cHi-C/chicQualityControl/sparsity.png" ftype="png" compare="sim_size" />
-
         </test>
     </tests>
     <help><![CDATA[