Update egapx

tools/ncbi_egapx/macros.xml

@@ -5,7 +5,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.2-alpha</token>
-    <token name="@VERSION_SUFFIX@">5</token>
+    <token name="@VERSION_SUFFIX@">7</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="edam_ontology">
         <edam_operations>

tools/ncbi_egapx/ncbi_egapx.xml

@@ -32,22 +32,24 @@
         #set genome_value = $cond_input_style.cond_genome_style.uri
     #end if
 genome: $genome_value
-taxid: $taxid
-    #if str($cond_rnaseq_style.rnaseq_style) == "list"
-        #set $reads_values = $rnaseq.split()
+taxid: $cond_input_style.taxid
+    #if str($cond_input_style.cond_rnaseq_style.rnaseq_style) == "history"
+        #set reads_values = $cond_input_style.cond_rnaseq_style.rnaseq
     #else
-        #set $reads_values = $rnaseq
+        #set reads_values = $cond_input_style.cond_rnaseq_style.rnaseq.split()
     #end if
 reads:
-    #for r in [x.strip() for x in $reads_values]
+    #for r in [str(rv).strip() for rv in $reads_values]
   - $r
     #end for
-    #if str($proteins) != "None"
-proteins: $proteins
+    #if str($cond_input_style.proteins) != "None"
+proteins: $cond_input_styleproteins
     #end if
-    #for row in $xtra.strip().split("\n")
+    #if str($cond_input_style.xtra) != "None"
+        #for row in str($cond_input_style.xtra).strip().split("\n")
 $row
-    #end for
+        #end for
+    #end if
 #end if
         ]]></configfile>
     </configfiles>
@@ -104,7 +106,7 @@ $row
                     </when>
                 </conditional>
                 <param name="proteins" type="data" format="fasta,fasta.gz" optional="true" label="Select a protein set"/>
-                <param name="xtra" type="text" area="true" label="Additional yaml to append to the egapx.yaml configuration"
+                <param name="xtra" type="text" area="true" optional="true" label="Additional yaml to append to the egapx.yaml configuration"
                     help="Not normally needed but useful for testing additional configuration elements">
                     <sanitizer invalid_char="">
                         <valid initial="string.printable"/>