changeset 1:c61c0d198e4a draft

Uploaded

--- a/samtools_calmd.xml	Wed Sep 24 10:43:00 2014 -0400
+++ b/samtools_calmd.xml	Mon Sep 29 11:38:42 2014 -0400
@@ -1,7 +1,7 @@
 <tool id="samtools_calmd" name="Recalculate" version="1.0.0">
     <description>MD/NM tags and '=' bases</description>
     <requirements>
-        <requirement type="package" version="1.0">samtools</requirement>
+        <requirement type="package" version="1.1">samtools</requirement>
     </requirements>
     <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
     <command><![CDATA[
@@ -30,7 +30,7 @@
             <when value="cached">
                 <param name="ref_fasta" type="select" label="Using reference genome">
                     <options from_data_table="fasta_indexes">
-                        <filter type="data_meta" column="value" key="dbkey" ref="input_bam" />
+                        <filter type="data_meta" column="0" key="dbkey" ref="input_bam" />
                         <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                     </options>
                 </param>
@@ -107,4 +107,4 @@
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
         </help>
-</tool>
\ No newline at end of file
+</tool>

--- a/tool_dependencies.xml	Wed Sep 24 10:43:00 2014 -0400
+++ b/tool_dependencies.xml	Mon Sep 29 11:38:42 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="samtools" version="1.0">
-	<repository changeset_revision="da217d52e81c" name="package_samtools_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  <package name="samtools" version="1.1">
+	<repository changeset_revision="c01b111a243b" name="package_samtools_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>