changeset 4:29f9b782727e draft default tip

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

--- a/macros.xml	Mon Mar 26 12:27:39 2018 -0400
+++ b/macros.xml	Thu Jan 23 08:09:46 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>

--- a/vcfleftalign.xml	Mon Mar 26 12:27:39 2018 -0400
+++ b/vcfleftalign.xml	Thu Jan 23 08:09:46 2020 -0500
@@ -5,33 +5,34 @@
   </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( $reference_source.ref_file.fields.path )
     #end if    
-   vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command>
+   vcfleftalign -r '${reference_fasta_filename}' -w "${window_size}" '${input_vcf}' > '${out_file1}'
+  ]]></command>
   <inputs>
-<param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
-    <conditional name="reference_source">
-       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
-         <option value="cached">Locally cached</option>
-         <option value="history">History</option>
-       </param>
-       <when value="cached">
-         <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"/>
-         </param>
-       </when>
-       <when value="history"> <!-- FIX ME!!!! -->
-         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-       </when>
-     </conditional>
-     <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" />
+    <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
+      <conditional name="reference_source">
+        <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+          <option value="cached">Locally cached</option>
+          <option value="history">History</option>
+        </param>
+        <when value="cached">
+          <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"/>
+          </param>
+        </when>
+        <when value="history"> <!-- FIX ME!!!! -->
+          <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        </when>
+      </conditional>
+    <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" />
   </inputs>
   <outputs>
     <data format="vcf" name="out_file1" />