# HG changeset patch
# User bgruening
# Date 1423329585 18000
# Node ID 09a565cfc192ab86455716ed2afa44c2f2f5f049
# Parent  fbe4eedec466fcc180880dda05c5c9500241a112
Uploaded

diff -r fbe4eedec466 -r 09a565cfc192 diamand.xml
--- a/diamand.xml	Sat Feb 07 05:32:30 2015 -0500
+++ b/diamand.xml	Sat Feb 07 12:19:45 2015 -0500
@@ -47,20 +47,6 @@
 ]]>
     </command>
     <inputs>
-        <conditional name="method">
-            <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)">
-                <option value="blastp">Align amino acid query sequences (blastp)</option>
-                <option value="blastx">Align DNA query sequences (blastx)</option>
-            </param>
-            <when value="blastp">
-                <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" />
-                <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" />
-            </when>
-            <when value="blastx">
-                <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" />
-                <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" />
-            </when>
-        </conditional>
 
         <param name="query" type="data" format="fasta" label="Input query file in FASTA format" />
 
@@ -85,6 +71,21 @@
           </when>  <!-- history -->
         </conditional>
 
+        <conditional name="method">
+            <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)">
+                <option value="blastp">Align amino acid query sequences (blastp)</option>
+                <option value="blastx">Align DNA query sequences (blastx)</option>
+            </param>
+            <when value="blastp">
+                <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" />
+                <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" />
+            </when>
+            <when value="blastx">
+                <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" />
+                <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" />
+            </when>
+        </conditional>
+
         <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)">
             <option value="BLOSUM45">BLOSUM45</option>
             <option value="BLOSUM50">BLOSUM50</option>
diff -r fbe4eedec466 -r 09a565cfc192 diamand_makedb.xml
--- a/diamand_makedb.xml	Sat Feb 07 05:32:30 2015 -0500
+++ b/diamand_makedb.xml	Sat Feb 07 12:19:45 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="bg_diamond_makedb" name="Diamond" version="0.6.13">
+<tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13">
     <description>Build database from a FASTA file</description>
     <requirements>
         <requirement type="package" version="0.6.13">diamond</requirement>
@@ -9,7 +9,9 @@
     diamond makedb 
         --threads "\${GALAXY_SLOTS:-12}"
         --in $infile
-        --db $outfile
+        --db ./database.dnmd
+    &&
+    mv ./database.dnmd $outfile
 ]]>
     </command>
     <inputs>
diff -r fbe4eedec466 -r 09a565cfc192 test-data/diamond_makedb_result1.dmnd
Binary file test-data/diamond_makedb_result1.dmnd has changed