diff variant_filtration.xml @ 6:35c00763cb5c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33

--- a/variant_filtration.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/variant_filtration.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,9 +1,10 @@
 <tool id="gatk2_variant_filtration" name="Variant Filtration" version="@VERSION@.0">
   <description>on VCF files</description>
-  <expand macro="requirements" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">
     #from binascii import hexlify
 
@@ -25,7 +26,7 @@
         #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name )  )
         -o '${ hexlify( $variant_filter ) }'
     #end for
-    
+
     #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask':
         -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}"
         -p '
@@ -33,9 +34,9 @@
         --maskName "${mask_rod_bind_type.mask_rod_name}"
         '
     #end if
-    
+
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp":
         -p '
@@ -62,8 +63,7 @@
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
-    
+
     <repeat name="variant_filters" title="Variant Filters">
         <param name="filter_expression" value="AB &lt; 0.2 || MQ0 &gt; 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &amp;lt;filterExpression&amp;gt;)">
             <sanitizer>
@@ -76,9 +76,7 @@
         <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &amp;lt;filterName&amp;gt;"/>
         <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &amp;lt;genotypeFilterExpression&amp;gt; and -G_filterName,--genotypeFilterName &amp;lt;genotypeFilterName&amp;gt; for filter type" />
     </repeat>
-    
 
-    
     <conditional name="mask_rod_bind_type">
       <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file">
         <option value="set_mask" selected="True">Set mask</option>
@@ -92,11 +90,10 @@
         <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &amp;lt;maskName&amp;gt;"/>
         <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &amp;lt;maskExtension&amp;gt;"/>
       </when>
-    </conditional>    
-    
-    
+    </conditional>
+
     <expand macro="gatk_param_type_conditional" />
-    
+
     <conditional name="cluster_snp_type">
       <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs">
         <option value="cluster_snp">Cluster SNPs</option>
@@ -110,9 +107,9 @@
         <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &amp;lt;clusterWindowSize&amp;gt;"/>
       </when>
     </conditional>
-    
+
     <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" />
-    
+
   </inputs>
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
@@ -133,7 +130,7 @@
           <param name="gatk_param_type_selector" value="basic" />
           <param name="cluster_snp_type_selector" value="do_not_cluster_snp" />
           <param name="missing_values_in_expressions_should_evaluate_as_failing" />
-          <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> 
+          <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
           <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" />
       </test>
   </tests>