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

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

--- a/print_reads.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/print_reads.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,9 +1,10 @@
 <tool id="gatk2_print_reads" name="Print Reads" version="@VERSION@.0">
   <description>on 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}"
@@ -20,7 +21,6 @@
     ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
     --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-6}
 
-
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
@@ -29,9 +29,9 @@
     #end if
     --disable_bam_indexing
    '
-   
+
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
@@ -50,10 +50,10 @@
         ${analysis_param_type.exception_if_no_tile}
         #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
             #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
-                --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}" 
+                --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
             #end if
             #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
-                --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}" 
+                --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
             #end if
         #end if
         ${analysis_param_type.simplify_bam}
@@ -67,7 +67,7 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" 
+    <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file"
         help="The input covariates table file which enables on-the-fly base quality score recalibration (intended for use with BaseRecalibrator files) (-BQSR,--BQSR)" />
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
@@ -92,10 +92,9 @@
         </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>
@@ -182,7 +181,7 @@
   </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" />