--- a/cactus_cactus.xml	Mon Nov 14 06:03:59 2022 +0000
+++ b/cactus_cactus.xml	Thu Jan 12 02:00:52 2023 +0000
@@ -1,5 +1,5 @@
 <tool id="cactus_cactus" name="Cactus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
-    <description>whole-genome multiple sequence alignment.</description>
+    <description>whole-genome multiple sequence alignment</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -61,15 +61,13 @@
             &&
             cactus-graphmap-join
             --binariesMode local
-            --gfaffix 
             --giraffe
             --maxCores  \${GALAXY_SLOTS:-4}
             --maxMemory \${GALAXY_MEMORY_MB:-8192}M
-            --outDir ./
             --outName alignment
             --reference $aln_mode.ref_level
             --vg alignment.vg
-            --wlineSep "." 
+            --outDir ./
             ./jobStore
         #else if $aln_mode.aln_mode_select == 'interspecies':
             ## Run cactus normally
@@ -92,14 +90,28 @@
                 <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes" />
             </when>
             <when value="intraspecies">
-                <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'." />
+                <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'.">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.letters,string.digits">
+                            <add value="_" />
+                        </valid>
+                    </sanitizer>
+                    <validator type="regex">[0-9a-zA-Z_]+</validator>
+                </param>
             </when>
         </conditional>
         <repeat name="in_seqs" title="Input genome">
-            <param name="label" type="text" value="" label="Genome Label" help="NO SPACES. Must match a label in the guide tree.">
+            <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree.">
+                <sanitizer invalid_char="">
+                    <valid initial="string.letters,string.digits">
+                        <add value="_" />
+                    </valid>
+                </sanitizer>
+                <validator type="regex">[0-9a-zA-Z_]+</validator>
             </param>
             <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
         </repeat>
+
         <!-- add an option for root -->
         <!-- root mr  -->
     </inputs>
@@ -138,7 +150,7 @@
             </repeat>
             <output name="out_hal">
                 <assert_contents>
-                    <has_size value="4783905" delta="200000" />
+                    <has_size value="4472551" delta="200000" />
                 </assert_contents>
             </output>
         </test>
@@ -235,12 +247,19 @@
         </test>
     </tests>
         <help><![CDATA[
+
+.. class:: infomark
+
 **What it does**
 
 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a
 reference-free whole-genome multiple alignment program. It can be used
 to progressively align a large number of genomes.
 
+-----
+
+.. class:: infomark
+
 **Usage**
 
 **Between-species mode (Progressive Cactus)**
@@ -253,9 +272,9 @@
 A Newick-formatted tree for human, chimp and gorilla genomes looks like
 this:
 
-::
+    ::
 
-   (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);
+        (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);
 
 The numbers are the branch lengths.
 
@@ -270,7 +289,11 @@
 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’
 dropdown.
 
-Unlike Between-species mode, Within-species mode depends on a predetermined reference genome
+Unlike Between-species mode, Within-species mode depends on a predetermined reference genome.
+
+-----
+
+.. class:: infomark
 
 **Input**
 
@@ -281,6 +304,10 @@
 fasta files that match the leaves on the guide tree. In the example
 above, you would use the label ‘human’ for the human fasta file.
 
+-----
+
+.. class:: infomark
+
 **Output**
 
 The main output of Cactus is in `HAL