Bug fix: PanTA (#7357)

* panta_fix branch

* Update file size in test

---------

Co-authored-by: Saim Momin <[email protected]>

Author: FMG0411

tools/panta/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">25.0</token>
     <xml name="requirements">
         <requirements>
@@ -27,4 +27,4 @@
             <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
         </creator>
     </xml>
-</macros>
+</macros>

tools/panta/panta.xml

@@ -13,12 +13,12 @@
 
         #if $input_type.input_type_selector == "gff":
             #for gff in $input_type.input_gff
-                #set identifier = re.sub('[^\s\w\-\\.]','_',str($gff.element_identifier))
-                ln -fs '$gff' '$input_directory/$identifier' &&
+                #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
+                cp '$gff' '$input_directory/$filename' &&
             #end for
         #elif $input_type.input_type_selector == "tsv":
-            #set identifier = re.sub('[^\s\w\-\\.]','_',str($input_type.input_tsv.element_identifier))
-            ln -fs '$input_type.input_tsv' '$input_directory/$identifier' &&
+            #set $filename = '%s.tsv' % re.sub('[^\w_-]', '_', str($input_type.input_tsv.element_identifier))
+            cp '$input_type.input_tsv' '$input_directory/$filename' &&
         #end if
 
         #if $mode.select_mode == "main":
@@ -402,7 +402,7 @@
             </output>
             <output name="core_gene_alignment" ftype="txt">
                 <assert_contents>
-                    <has_n_lines n="96690" delta='3'/>
+                    <has_n_lines n="96130" delta='3'/>
                 </assert_contents>
             </output>
             <output name="pan_genome_reference" ftype="txt">
@@ -709,4 +709,4 @@ PanTA builds the pangenome of a large collection of genomes and adds a set of ne
         <citation type="doi">10.6084/m9.figshare.23724705</citation>
     </citations>
     <expand macro="creator"/>
-</tool>
+</tool>