# HG changeset patch
# User iuc
# Date 1579785062 18000
# Node ID 166c4f50525fee06c0b1306b68b9e0250cf5601c
# Parent  6f6bf10618d74929f4a0a138c259573a55964365
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit 36e9065027cc7bf721e9d203208477ee88906c57"

diff -r 6f6bf10618d7 -r 166c4f50525f macros.xml
--- a/macros.xml	Mon Mar 26 12:29:13 2018 -0400
+++ b/macros.xml	Thu Jan 23 08:11:02 2020 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.0.0_rc1">vcflib</requirement>
+            <requirement type="package" version="1.0.0_rc3">vcflib</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -10,10 +10,10 @@
             <exit_code range="1:" level="fatal" />
         </stdio>
     </xml>
-   <token name="@WRAPPER_VERSION@">1.0.0_rc1</token>
-   	<xml name="citations">
-   	     <citations>
-             <citation type="bibtex">
+   <token name="@WRAPPER_VERSION@">1.0.0_rc3</token>
+       <xml name="citations">
+           <citations>
+               <citation type="bibtex">
 @misc{Garrison2015,
   author = {Garrison, Erik},
   year = {2015},
@@ -22,8 +22,8 @@
   journal = {GitHub repository},
   url = {https://github.com/ekg/vcflib},
 }
-             </citation>
-   	     </citations>
-   	</xml>
+            </citation>
+        </citations>
+        </xml>
     <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token>
 </macros>
diff -r 6f6bf10618d7 -r 166c4f50525f vcfvcfintersect.xml
--- 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" />