Mercurial > repos > iuc > hal_halpctid

diff hal_halPctId.xml @ 2:95f0cb8ccfe1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 30ac0af6dfa729277011bcd73cd5560efa03fb97
author iuc
date Wed, 18 Mar 2026 15:21:14 +0000
parents 07c1e49a89de
children
line wrap: on
line diff
--- a/hal_halPctId.xml	Thu Mar 05 11:35:31 2026 +0000
+++ b/hal_halPctId.xml	Wed Mar 18 15:21:14 2026 +0000
@@ -11,7 +11,7 @@
             --numSamples $numSamples
             --seed $seed
             ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
-            '$input_hal' '$refGenome' | tr ',' '\t' > '$out_file' 
+            '$input_hal' '$refGenome' | sed $'s/, */\t/g' > '$out_file' 
     ]]></command>
     <inputs>
         <expand macro="input_hal"/>
@@ -29,9 +29,9 @@
             <param name="seed" value="100"/>
             <output name="out_file" ftype="tabular">
                 <assert_contents>
-                    <has_line line="Genome&#009; IdenticalSites&#009; AlignedSites&#009; PercentIdentity"/>
-                    <has_line line="Genome_1&#009; 856475&#009; 856475&#009; 100"/>
-                    <has_line line="Genome_2&#009; 374132&#009; 374132&#009; 100"/>
+                    <has_line line="Genome&#009;IdenticalSites&#009;AlignedSites&#009;PercentIdentity"/>
+                    <has_line line="Genome_1&#009;856475&#009;856475&#009;100"/>
+                    <has_line line="Genome_2&#009;374132&#009;374132&#009;100"/>
                     <has_n_lines n="4"/>
                 </assert_contents>
             </output>
@@ -43,9 +43,9 @@
             <param name="seed" value="100"/>
             <output name="out_file" ftype="tabular">
                 <assert_contents>
-                    <has_line line="Genome&#009; IdenticalSites&#009; AlignedSites&#009; PercentIdentity"/>
-                    <has_line line="Genome_1&#009; 839&#009; 839&#009; 100"/>
-                    <has_line line="Genome_2&#009; 339&#009; 339&#009; 100"/>
+                    <has_line line="Genome&#009;IdenticalSites&#009;AlignedSites&#009;PercentIdentity"/>
+                    <has_line line="Genome_1&#009;839&#009;839&#009;100"/>
+                    <has_line line="Genome_2&#009;339&#009;339&#009;100"/>
                     <has_n_lines n="4"/>
                 </assert_contents>
             </output>