# HG changeset patch
# User iuc
# Date 1579784224 0
# Node ID 00f74c1efa2d6d8dfa0c62fb7c7aabdd35bb8264
# Parent  25d297ce9ccbe2f8d800d7236c0dec4976a58d1e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo commit 36e9065027cc7bf721e9d203208477ee88906c57"

diff -r 25d297ce9ccb -r 00f74c1efa2d macros.xml
--- a/macros.xml	Mon Mar 26 12:14:25 2018 -0400
+++ b/macros.xml	Thu Jan 23 12:57:04 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>
diff -r 25d297ce9ccb -r 00f74c1efa2d vcfgeno2haplo.xml
--- a/vcfgeno2haplo.xml	Mon Mar 26 12:14:25 2018 -0400
+++ b/vcfgeno2haplo.xml	Thu Jan 23 12:57:04 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    
-  vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
+  vcfgeno2haplo ${output_option} -w ${window_size} -r "${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">
@@ -24,23 +25,23 @@
            <options from_data_table="fasta_indexes">
              <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
            </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>
-	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
-	   <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
-		<validator type="unspecified_build" />
-		<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
-	   -->
-	 </param>
+         <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
+           <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
+           <validator type="unspecified_build" />
+           <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+           -->
+         </param>
        </when>
        <when value="history"> <!-- FIX ME!!!! -->
          <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
+         <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
        </when>
      </conditional>
      <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
      <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
-<!--       <option value=" ">Output entire haplotype</option>
+     <!-- <option value=" ">Output entire haplotype</option>
        <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
      </param> -->
   </inputs>
@@ -56,7 +57,7 @@
       <param name="ref_file" value="vcflib-test-genome-phix.fa" />
       <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
     </test>
-    </tests>
+  </tests>
   <help>
 
 Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.