diff vcfvcfintersect.xml @ 5:166c4f50525f draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"

--- a/vcfvcfintersect.xml	Mon Mar 26 12:29:13 2018 -0400
+++ b/vcfvcfintersect.xml	Thu Jan 23 08:11:02 2020 -0500
@@ -5,20 +5,20 @@
     </macros>
     <expand macro="requirements"/>
     <expand macro="stdio" />
-    <command>
+    <command><![CDATA[
         #set $reference_fasta_filename = "localref.fa"
         #if str( $reference_source.reference_source_selector ) == "history":
-           ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+           ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
         #else:
            #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
         #end if
 
         #if $adv_options.adv_options_selector == "use_adv_controls":
-            vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
+            vcfintersect '${adv_options.adv_options_input}' ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}'
         #else:
-            vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
+            vcfintersect ${loci} ${invert} -r '${reference_fasta_filename}' -w "${window_size}" ${isect_union} '${vcf_input1}' '${vcf_input2}' > '${out_file1}'
         #end if
-    </command>
+    ]]></command>
     <inputs>
         <!-- selecting refernce source -->
         <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" />