diff macros.xml @ 27:9f164587a92f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870

--- a/macros.xml	Thu May 04 11:34:13 2017 -0400
+++ b/macros.xml	Tue Jun 06 11:44:38 2017 -0400
@@ -1,20 +1,41 @@
 <macros>
-    <token name="@DEPENDENCY_VERSION@">1.0.2.29</token>
+    <token name="@DEPENDENCY_VERSION@">1.1.0</token>
 
     <xml name="citations">
         <citations>
             <citation type="bibtex">
-              @misc{1207.3907,
-                  Author = {Erik Garrison},
-                  Title = {Haplotype-based variant detection from short-read sequencing},
-                  Year = {2012},
-                  Eprint = {arXiv:1207.3907},
-                  url = {http://arxiv.org/abs/1207.3907}
-              }
+                @misc{1207.3907,
+                    Author = {Erik Garrison},
+                    Title = {Haplotype-based variant detection from short-read sequencing},
+                    Year = {2012},
+                    Eprint = {arXiv:1207.3907},
+                    url = {http://arxiv.org/abs/1207.3907}
+                }
             </citation>
         </citations>
     </xml>
-    
+    <xml name="validation">
+        <validator type="unspecified_build" />
+        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+    </xml>
+    <xml name="input_bam">
+        <conditional name="batchmode">
+            <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF file for each input BAM file. Selecting the merge option will produce one VCF file for all input BAM files." display="radio">
+                <option value="individual" selected="True">Run individually</option>
+                <option value="merge">Merge output VCFs</option>
+            </param>
+            <when value="individual">
+                <param name="input_bams" type="data" format="bam" label="BAM file">
+                    <yield />
+                </param>
+            </when>
+            <when value="merge">
+                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
+                    <yield />
+                </param>
+            </when>
+        </conditional>
+    </xml>
     <xml name="par_min_cov">
         <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site"
                help="default=0" argument="--coverage" />