--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blastn_to_scaffold.xml	Sun Jun 21 14:41:10 2015 -0400
@@ -0,0 +1,47 @@
+<tool id="blastn2scaffold" name="blastn_to_scaffold" version="0.1.0">
+<description>Generate DNA scaffold from blastn alignment of Contigs</description>
+<requirements>
+</requirements>
+<command interpreter="python">
+        blastn_to_scaffold.py --sequences $sequences
+                              --guideSequence $guideSequence
+                              --blastn-tab $blastn_tab
+                              --output $output
+</command>
+<inputs>
+<param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> 
+<param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> 
+<param name="blastn_tab"  type="data" format="tabular" label="Select a blastn output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> 
+
+</inputs>
+<outputs>
+ <data format="fasta" name="output"/>
+</outputs>
+
+
+<tests>
+  <test>
+    <param name="sequences" value="contigs.fa" ftype="fasta"/>
+    <param name="blastn_tab" value="blastn.tab" ftype="tabular"/>
+    <param name="guideSequence" value="guideSequence.fa" ftype="tabular"/>
+    <output name="output" file="assembly.fa" ftype="fasta"/>
+  </test>
+</tests>
+        
+
+<help>
+
+
+**What it Does**
+This tool start from DNA contigs that aligned to a subject DNA sequence through blastn.
+The contigs must be provided in fasta format. The blastn output must be tabular, the 12 standard column plus column 13 with the length of the blastn subject.
+The sequence used to blastn the contigs must be provided to serve as a guide to the final assembly
+The final assembly is a DNA sequence.
+Nucleotides of the guide sequence which were not covered by contigs are in small letters in the output assembly.
+
+
+**Attribution**
+This Galaxy tool was created by drosofff@gmail.com on 9/06/2015
+</help>
+
+</tool>