diff snpindex.xml @ 5:14561eb803a5 draft

Uploaded v3.0.1b (still working on this prior to main Tool Shed release)

--- a/snpindex.xml	Wed Sep 28 10:49:02 2016 -0400
+++ b/snpindex.xml	Fri Oct 21 10:55:40 2016 -0400
@@ -4,9 +4,11 @@
       <requirement type="package" version="2013-05-09">gmap</requirement>
   </requirements>
   <version_command>snpindex --version</version_command>
-  <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>
+  <command detect_errors="exit_code" interpreter="bash"><![CDATA[
+$shscript 2>1 1> $output
+  ]]></command>
   <configfiles>
-    <configfile name="shscript">
+    <configfile name="shscript"><![CDATA[
 #!/bin/bash
 #set $ds = chr(36)
 #set $gt = chr(62)
@@ -41,7 +43,7 @@
 snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
 echo snpindex -D  $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
 #end if
-    </configfile>
+    ]]></configfile>
   </configfiles>
   <inputs>
     <conditional name="refGenomeSource">
@@ -51,7 +53,7 @@
       </param>
       <when value="indexed">
         <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
-          <options from_file="gmap_indices.loc">
+          <options from_data_table="gmap_indices">
             <column name="uid" index="0" />
             <column name="dbkey" index="1" />
             <column name="name" index="2" />