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

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

--- a/reduce_reads.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/reduce_reads.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,9 +1,10 @@
 <tool id="gatk2_reduce_reads" name="Reduce Reads" version="@VERSION@.0">
   <description>in BAM files</description>
-  <expand macro="requirements" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${output_log}"
@@ -30,7 +31,7 @@
     --disable_bam_indexing
    '
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
@@ -90,9 +91,9 @@
         </param>
       </when>
     </conditional>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
     <conditional name="analysis_param_type">
       <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
         <option value="basic" selected="True">Basic</option>
@@ -136,7 +137,7 @@
   </outputs>
   <tests>
       <test>
-          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 
+          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
           <param name="reference_source_selector" value="history" />
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />