diff vcfprimers.xml @ 4:7f941e486881 draft default tip

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

--- a/vcfprimers.xml	Mon Mar 26 12:15:49 2018 -0400
+++ b/vcfprimers.xml	Thu Jan 23 12:58:37 2020 +0000
@@ -5,14 +5,15 @@
   </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( $reference_source.ref_file.fields.path )
     #end if    
-   vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}"</command>
+   vcfprimers -f '${reference_fasta_filename}' -l "${primer_length}" '${input_vcf}' > '${out_file1}'
+  ]]></command>
   <inputs>
 <param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" />
     <conditional name="reference_source">
@@ -24,7 +25,7 @@
          <param name="ref_file" type="select" label="Select reference genome">
            <options from_data_table="fasta_indexes">
            </options>
-	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
          </param>
        </when>
        <when value="history"> <!-- FIX ME!!!! -->