--- a/cactus_cactus.xml	Tue Sep 13 00:17:17 2022 +0000
+++ b/cactus_cactus.xml	Tue Sep 20 05:38:05 2022 +0000
@@ -6,25 +6,6 @@
     <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        ## Check the FASTA headers
-        ## This is only necessary in pangenome mode
-        #if $aln_mode.aln_mode_select == 'intraspecies':
-            #for $seq in $in_seqs:
-                if
-                #if $seq.fasta.is_of_type('fasta.gz'):
-                    zgrep
-                #else
-                    grep
-                #end if
-                "^>" $seq.fasta | grep -q "[[:space:]]" ; then
-                    echo "Error parsing input FASTA." ;
-                    echo "Pangenome mode fails if there are spaces in the header." ;
-                    echo "Please remove them with the NormalizeFasta tool." ;
-                    exit 1 
-                    ; fi &&
-            #end for
-        #end if
-
         ## Set up seqfile
         
         #if $aln_mode.aln_mode_select == 'interspecies':
@@ -190,8 +171,8 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- FASTA header -->
-        <test expect_exit_code="1" expect_failure="true">
+        <!-- FASTA header with spaces (used to fail) -->
+        <test expect_num_outputs="1">
             <conditional name="aln_mode">
                 <param name="aln_mode_select" value="intraspecies"/>
             </conditional>
@@ -203,6 +184,11 @@
                 <param name="label" value="badheader2"/>
                 <param name="fasta" value="bh2.fasta.gz"/>
             </repeat>
+            <output name="out_hal">
+                <assert_contents>
+                    <has_size value="3382274" delta="200000" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
         <help><![CDATA[
@@ -241,9 +227,6 @@
 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’
 dropdown.
 
-⚠️ To use pangenome mode, you will have to remove spaces from the headers in your FASTA file.
-You can do this with the NormalizeFasta tool.
-
 **Input**
 
 The developers recommend soft-masking your genomes with RepeatMasker