diff depth_of_coverage.xml @ 13:669a23f1f4b5 draft

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

--- a/depth_of_coverage.xml	Thu May 14 22:47:18 2015 -0400
+++ b/depth_of_coverage.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
+<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
   <description>on BAM files</description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -8,12 +8,7 @@
   <command interpreter="python">gatk2_wrapper.py
    ##--max_jvm_heap_fraction "1"
    --stdout "${output_log}"
-   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
-       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-       #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
-           -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
-       #end if
-   #end for
+   @BAM_INPUTS@
    -p '
    @JAR_PATH@
     -T "DepthOfCoverage"
@@ -129,12 +124,7 @@
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
-              <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
-            </param>
-        </repeat>
+        <expand macro="input_bams_cached" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk2_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
@@ -143,9 +133,8 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file" />
-        </repeat>
+
+        <expand macro="input_bams_history" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>