changeset 4:2b86cb8d0d51 draft

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

--- a/macros.xml	Mon Mar 26 12:12:34 2018 -0400
+++ b/macros.xml	Thu Jan 23 12:54:30 2020 +0000
@@ -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>

--- a/vcfcheck.xml	Mon Mar 26 12:12:34 2018 -0400
+++ b/vcfcheck.xml	Thu Jan 23 12:54:30 2020 +0000
@@ -7,14 +7,15 @@
     <stdio>
         <regex match="index file" source="stderr" level="warning"/>
     </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
-        vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
+        vcfcheck $failure_selector -f '${reference_fasta_filename}' '${input_vcf}' > '${out_file1}'
+    ]]></command>
     <inputs>
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">