diff hal_halStats.xml @ 1:a9eb29f924e1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf

--- a/hal_halStats.xml	Fri Feb 06 10:48:53 2026 +0000
+++ b/hal_halStats.xml	Thu Mar 05 11:30:42 2026 +0000
@@ -7,11 +7,11 @@
     <expand macro="stdio"/>
     <command detect_errors="aggressive"><![CDATA[
         set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure.
-        ( ## echo headers for specific numerical data
+        ## echo headers for specific numerical data
         #if $mode.option == '--baseComp':
-            echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts';
+            echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts' >> '$out_file' &&
         #else if $mode.option == '--numSegments':
-            echo -e 'numTopSegments\tnumBottomSegments';
+            echo -e 'numTopSegments\tnumBottomSegments' >> '$out_file' &&
         #end if
         halStats
             #if $mode.option == '--allCoverage':
@@ -60,13 +60,13 @@
                 --topSegments '$mode.topSegments'
             #end if
             '$input_hal'
-        ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
-        #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage':
-            | tr ',' '\t'
-        #else if $mode.option == '--numSegments':
-            | tr ' ' '\t' ## Replace spaces
-        #end if
-        ) > '$out_file'
+            ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
+            #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage':
+                | tr ',' '\t'
+            #else if $mode.option == '--numSegments':
+                | tr ' ' '\t' ## Replace spaces
+            #end if
+            >> '$out_file'
     ]]></command>
     <inputs>
         <expand macro="input_hal"/>