--- a/blat.xml	Thu May 31 11:25:53 2018 -0400
+++ b/blat.xml	Mon Jul 09 13:07:54 2018 -0400
@@ -1,70 +1,31 @@
 <?xml version="1.0"?>
-<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="36">
-    <description>BLAST-like sequence alignment tool</description>
+<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.1">
+    <description>Standalone blat sequence search command line tool</description>
     <requirements>
-      <requirement type="package" version="36">blat</requirement>
+      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if str($reference_source.reference_source_selector) == "history":
-            ## blat depends on file extension
-            #if $reference_source.database.is_of_type("fasta"):
-                #set $reference_fasta_filename = "localref.fa"
-            #elif $reference_source.database.is_of_type("twobit"):
-                #set $reference_fasta_filename = "localref.2bit"
-            #else
-                #set $reference_fasta_filename = "localref"
-            #end if
-
+            #set $reference_fasta_filename = "localref.fa" 
             ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
       #else:
             #set $reference_fasta_filename = str($reference_source.database.fields.path)
       #end if
-
-      blat
-
+      blat 
+            #if $noHead == "yes"
+            -noHead
+            #end if
             -q=$query_type
             -t=$database_type
-
-            ${oneOff}
-
-            #if str($minScore)
-              -minScore=${minScore}
-            #end if
-
-            -maxGap=${maxGap}
-
-            #if str($repMatch)
-              -repMatch=${repMatch}
-            #end if
-
             #if $mask_type.mask == "file.out":
-                  -mask='${mask_type.mask_file}'
+                  -mask=$mask_type.mask_file
             #else:
                   -mask=$mask_type.mask
             #end if
-
-            #if str($dots)
-              -dots=${dots}
-            #end if
-
-            ${trimT}
-            ${noTrimA}
-            ${trimHardA}
-            ${fastMap}
-            ${fine}
-
-            #if str($maxIntron)
-             -maxIntron=${maxIntron}
-            #end if
-
-            ${extendThroughN}
-
             '$reference_fasta_filename'
             '${query}'
-
-            -out=${out}
-
-            '${output}'
+            output
+      && sort -k 10,10 -k 12,12n output > '${output_sorted}'
 ]]></command>
       <inputs>
             <conditional name="reference_source">
@@ -81,10 +42,10 @@
                         </param>
                   </when>
                   <when value="history">
-                        <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
+                        <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" />
                   </when>
             </conditional>
-            <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
+            <param type="data" name="query" format="fasta,twobit" label="Query data, either a .fa, .nib or .2bit file"/>
             <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>
@@ -97,10 +58,10 @@
                   <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 argument="-oneOff" type="boolean" truevalue="-oneOff=1" falsevalue="" label="If set, this allows one mismatch in tile and still triggers an alignments" />
-            <param argument="-minScore" type="integer" value="30" label="Minimum score" help="It is the matches minus the mismatches minus some sort of gap penalty" />
-            <param argument="-maxGap" type="integer" value="2" min="0" max="3" label="Maximum gap between tiles in a clump" help="Usually set from 0 to 3. Only relevant for minMatch > 1" />
-            <param argument="-repMatch" type="integer" value="" optional="true" label="Number of repetitions of a tile allowed before it is marked as overused" help="Typically this is 256 for tileSize 12, 1024 for tileSize 11, 4096 for tileSize 10. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate" />
+            <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>
             <conditional name="mask_type">
                   <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
@@ -115,39 +76,11 @@
                   <when value="out" />
                   <when value="file.out">
                         <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" />
-                  </when>
+                  </when>  
             </conditional>
-            <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" />
-            <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" />
-            <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" />
-            <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" />
-            <param argument="-fastMap" type="boolean" truevalue="-fastMap" falsevalue="" label="Run for fast DNA/DNA remapping" help="It does not allow introns and require high %ID. Query sizes must not exceed 5000" />
-            <param argument="-fine" type="boolean" truevalue="-fine" falsevalue="" label="Refine search for small initial and terminal exons" help="For high-quality mRNAs. Not recommended for ESTs" />
-            <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" />
-            <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" />
-            <param name="out" type="select" label="Select output file format (-out)">
-                <option value="psl">Tab-separated format, no sequence (psl)</option>
-                <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option>
-                <option value="axt">Blastz-associated axt format (axt)</option>
-                <option value="maf">Multiz-associated maf format (maf)</option>
-                <option value="sim4">Similar to sim4 format (sim4)</option>
-                <option value="wublast">Similar to WU-BLAST format (wublast)</option>
-                <option value="blast">Similar to NCBI BLAST format (blast)</option>
-                <option value="blast8">NCBI BLAST tabular format (blast8)</option>
-                <option value="blast9">NCBI BLAST tabular format with comments (blast9)</option>
-            </param>
       </inputs>
       <outputs>
-            <data name="output" format="tabular" label="${tool.name} on ${on_string}">
-                <change_format>
-                    <when input="out" value="psl" format="psl" />
-                    <when input="out" value="axt" format="axt" />
-                    <when input="out" value="maf" format="maf" />
-                    <when input="out" value="sim4" format="txt" />
-                    <when input="out" value="wublast" format="txt" />
-                    <when input="out" value="blast" format="txt" />
-                </change_format>
-            </data>
+            <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
       </outputs>
   <tests>
       <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
@@ -155,53 +88,44 @@
             <param name="reference_source_selector" value="history" />
             <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="database_type" value="dnax" />    
+            <param name="query_type" value="rnax" />     
+            <param name="noHead" value="yes" />
             <param name="mask" value="lower" />
-            <param name="out" value="psl -noHead" />
-            <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl" sort="True"/>
+            <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
       </test>
       <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->
       <test>
             <param name="reference_source_selector" value="history" />
             <param name="database" value="dbia3/dbia3.fa" />
             <param name="query" value="dbia3/dmel-transcript.fa" />
-            <param name="database_type" value="dnax" />
-            <param name="query_type" value="rnax" />
+            <param name="database_type" value="dnax" />    
+            <param name="query_type" value="rnax" />     
+            <param name="noHead" value="yes" />
             <param name="mask" value="lower" />
-            <param name="out" value="psl -noHead" />
-            <param name="maxIntron" value="" />
-            <output name="output" value="dbia3/dbia3.sorted.psl" sort="True"/>
+            <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
       </test>
       <!-- test on the database masked by repeat masker -->
       <test>
             <param name="reference_source_selector" value="history" />
             <param name="database" value="dbia3/dbia3_masked.2bit" />
             <param name="query" value="dbia3/dmel-transcript.fa" />
-            <param name="database_type" value="dnax" />
-            <param name="query_type" value="rnax" />
-            <param name="oneOff" value="false" />
-            <param name="minScore" value="30" />
-            <param name="maxGap" value="2" />
-            <param name="trimT" value="false" />
-            <param name="noTrimA" value="false" />
-            <param name="fine" value="false" />
-            <param name="maxIntron" value="750000" />
-            <param name="extendThroughN" value="false" />
+            <param name="database_type" value="dnax" />    
+            <param name="query_type" value="rnax" />     
+            <param name="noHead" value="yes" />
             <param name="mask" value="file.out" />
             <param name="mask_file" value="dbia3/dbia3_RM.out" />
-            <param name="out" value="psl -noHead" />
-            <output name="output" value="dbia3/dbia3_masked.sorted.psl"/>
+            <output name="output_sorted" value="dbia3/dbia3_masked.sorted.psl" />
       </test>
 
-  </tests>
+  </tests> 
   <help>
         <![CDATA[
 BLAT
 ====
-BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
+BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. 
 
-blat (version: v36)- Standalone blat sequence search command line tool.
+blat (version: v340)- Standalone blat sequence search command line tool. 
 -------------------------------------------------------------------------
 
 usage:
@@ -215,20 +139,25 @@
    -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.
+   output.psl is the name of the output file.  
 
 documentation:
 ++++++++++++++
 
-See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
+See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) 
 
 Source code:
 ++++++++++++
 
 http://hgdownload.cse.ucsc.edu/admin/exe/
 
-]]></help>
+]]></help>  
 <citations>
       <citation type="doi">10.1101/gr.229202</citation>
-</citations>
+</citations> 
 </tool>
+             
+            
+
+               
+    
\ No newline at end of file