diff variant_apply_recalibration.xml @ 13:669a23f1f4b5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e

--- a/variant_apply_recalibration.xml	Thu May 14 22:47:18 2015 -0400
+++ b/variant_apply_recalibration.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.0">
+<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.1">
   <description></description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -8,8 +8,8 @@
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${output_log}"
-    #for $var_count, $variant in enumerate( $reference_source.variants ):
-        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+    #for $var_count, $variant in enumerate( $reference_source.input_variants ):
+        -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
     #end for
    -p '
    @JAR_PATH@
@@ -46,9 +46,7 @@
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
-          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/>
-        </repeat>
+        <expand macro="input_variants" />
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
@@ -59,9 +57,7 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
-          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
-        </repeat>
+        <expand macro="input_variants" />
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />