--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blat.xml	Wed Apr 12 17:47:43 2017 -0400
@@ -0,0 +1,122 @@
+<?xml version="1.0"?>
+<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
+    <description>Standalone blat sequence search command line tool</description>
+    <requirements>
+      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    blat 
+        #if $noHead == "yes"
+          -noHead
+        #end if
+        -q=$query_type
+        -t=$database_type
+        -mask=$mask
+        '${database}'
+        '${query}'
+        output
+    && sort -k 10,10 -k 12,12n output > '${output_sorted}'
+]]></command>
+      <inputs>
+            <param type="data" name="database" format="fasta" />
+            <param type="data" name="query" format="fasta" />
+            <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
+                  <option value="dna">dna - DNA sequence</option>
+                  <option value="prot">prot - protein sequence</option>
+                  <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
+            </param>
+            <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q">
+                  <option value="dna">dna - DNA sequence </option>
+                  <option value="rna">rna - RNA sequence</option>
+                  <option value="prot">prot - protein sequence</option>
+                  <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
+                  <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
+            </param>
+            <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." >
+                  <option value="yes" selected="true">Yes, suppresses .psl header</option>
+                  <option value="no">No, do not suppresses .psl header</option>
+            </param>
+            <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
+                  but may extend through it in nucleotide searches.  Masked areas
+                  are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
+                  <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
+                  <option value="upper">upper - mask out upper-cased sequence</option>
+                  <option value="out">out - mask according to database.out RepeatMasker .out file</option>
+                  <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
+            </param>
+      </inputs>
+      <outputs>
+            <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
+      </outputs>
+  <tests>
+      <test>
+            <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
+            <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
+            <param name="database_type" value="dnax" />    
+            <param name="query_type" value="rnax" />     
+            <param name="noHead" value="true" />
+            <param name="mask" value="lower" />
+            <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
+      </test>
+      <test>
+            <param name="database" value="dbia3/dbia3.fa" />
+            <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
+            <param name="database_type" value="dnax" />    
+            <param name="query_type" value="rnax" />     
+            <param name="noHead" value="true" />
+            <param name="mask" value="lower" />
+            <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
+      </test>
+
+  </tests> 
+  <help>
+        <![CDATA[
+BLAT
+====
+BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. 
+
+blat (version: v340)- Standalone blat sequence search command line tool. 
+-------------------------------------------------------------------------
+
+usage:
+++++++
+
+  $ blat database query [-ooc=11.ooc] output.psl
+
+where:
+   database and query are each either a .fa, .nib or .2bit file,
+   or a list of these files with one file name per line.
+   -ooc=11.ooc tells the program to load over-occurring 11-mers from
+   an external file.  This will increase the speed
+   by a factor of 40 in many cases, but is not required.
+   output.psl is the name of the output file.  
+
+documentation:
+++++++++++++++
+
+See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) 
+
+Source code:
+++++++++++++
+
+http://hgdownload.cse.ucsc.edu/admin/exe/
+
+]]></help>  
+<citations>
+      <citation type="bibtex">@article{kent2002blat,
+  title={BLAT—the BLAST-like alignment tool},
+  author={Kent, W James},
+  journal={Genome research},
+  volume={12},
+  number={4},
+  pages={656--664},
+  year={2002},
+  publisher={Cold Spring Harbor Lab}
+      }</citation>
+</citations> 
+</tool>
+             
+            
+
+               
+    
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