diff vcfgeno2haplo.xml @ 2:aa3ca755f70d draft

Uploaded

--- a/vcfgeno2haplo.xml	Tue Jun 10 12:37:48 2014 -0400
+++ b/vcfgeno2haplo.xml	Wed Jun 11 16:16:43 2014 -0400
@@ -10,7 +10,7 @@
     #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">
@@ -37,7 +37,7 @@
        </when>
      </conditional>
      <param name="window_size" type="text" size="4" value="30" label="compare records up to this many bp away (window size)" help="--window-size option (default = 30)" />
-     <param name="output_option" type="boolean" truevalue="-o" label="What to report?" help="--only-variants option" />
+     <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="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
      </param> -->
@@ -52,9 +52,9 @@
     <test>
       <param name="reference_source_selector" value="history" />
       <param name="output_option" value="true" />
-      <param name="window_size" value="10000" />
-      <param name="input_vcf" value="vcflib-chr20-X.vcf"/>
-      <param name="ref_file" value="vcflib-human-reference-chr20-XY.fa" />
+      <param name="window_size" value="5000" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
       <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
     </test>
     </tests>