# HG changeset patch
# User richard-burhans
# Date 1739819839 0
# Node ID 21d4de0e41fc93e782927aa5cbaa0c36d4416e72
# Parent  8ada50a892fa35547f1932a417ab8b92fbc26fb7
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bdcd7b1991f872540fb5f87ee945077b5ca68780

diff -r 8ada50a892fa -r 21d4de0e41fc ncbi_egapx.xml
--- a/ncbi_egapx.xml	Thu Jan 23 21:23:14 2025 +0000
+++ b/ncbi_egapx.xml	Mon Feb 17 19:17:19 2025 +0000
@@ -59,7 +59,7 @@
          <environment_variable name="NXF_DEBUG">3</environment_variable>
     </environment_variables>
     <configfiles>
-        <configfile name="reads_config"><![CDATA[
+        <configfile name="reads_config"><![CDATA[#slurp
         #if $cond_input_style.input_style == "fillform" and $cond_input_style.cond_rnaseq_style.rnaseq_style == "history"
             #import re
             #for $idx, $read in enumerate($cond_input_style.cond_rnaseq_style.rnaseq)
@@ -82,39 +82,41 @@
                 #end for
             #end for
         #end if
-        ]]></configfile>
-        <configfile name="egapx_config"><![CDATA[
-#if $cond_input_style.input_style == "fillform"
-    #import re
-    #if $cond_input_style.cond_genome_style.genome_style == "history"
-        #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.element_identifier)) + "." + $genome.ext
-    #else if $cond_input_style.cond_genome_style.genome_style == "indexed"
-        #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.fields.element_identifier)) + "." + $genomefields.ext
-    #else
-        #set genome_value = $uri
-    #end if
+        #silent pass]]></configfile>
+        <configfile name="egapx_config"><![CDATA[#slurp
+        #if $cond_input_style.input_style == "fillform"
+            #import re
+            #if $cond_input_style.cond_genome_style.genome_style == "history"
+                #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.element_identifier)) + "." + $genome.ext
+            #else if $cond_input_style.cond_genome_style.genome_style == "indexed"
+                #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.fields.element_identifier)) + "." + $genomefields.ext
+            #else
+                #set genome_value = $uri
+            #end if
 # yaml generated by ncbi_egapx.xml
 genome: $genome_value
 taxid: $taxid
-    #if $cond_input_style.cond_rnaseq_style.rnaseq_style == "history"
+            #if $cond_input_style.cond_rnaseq_style.rnaseq_style == "history"
 reads: $reads_config
     #else
 reads:
         #set reads_values = $rnaseq.split()
         #for $read in [str(rv).strip() for rv in $reads_values]
   - $read
-        #end for
-    #end if
-    #if str($cond_input_style.proteins) != "None"
+                #end for
+            #end if
+            #if str($cond_input_style.proteins) != "None"
 proteins: $cond_input_style.proteins
-    #end if
-    #if str($cond_input_style.extra) != "None"
-        #for row in str($cond_input_style.extra).strip().split("\n")
+            #end if
+            #if str($cond_input_style.extra) != "None"
+                #for row in str($cond_input_style.extra).strip().split("\n")
+                    #if $row
 $row
-        #end for
-    #end if
-#end if
-        ]]></configfile>
+                    #end if
+                #end for
+            #end if
+        #end if
+        #silent pass]]></configfile>
     </configfiles>
     <inputs>
         <conditional name="cond_input_style">