# HG changeset patch
# User iuc
# Date 1498275189 14400
# Node ID dede60f744f488ba07670843292d330e8246c09d
# Parent  545bc7831814f9e8a149fd2fc550bc7020e69eef
planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7

diff -r 545bc7831814 -r dede60f744f4 README.rst
diff -r 545bc7831814 -r dede60f744f4 blat.xml
--- a/blat.xml	Thu Jun 01 16:31:08 2017 -0400
+++ b/blat.xml	Fri Jun 23 23:33:09 2017 -0400
@@ -1,29 +1,42 @@
 <?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>
+<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-0">
+    <description>BLAST-like sequence alignment tool</description>
     <requirements>
-      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
+      <requirement type="package" version="35">blat</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if str($reference_source.reference_source_selector) == "history":
-            #set $reference_fasta_filename = "localref.fa" 
+            ## 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 $reference_fasta_filename = "localref"
+            #end if
+
             ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
       #else:
             #set $reference_fasta_filename = str($reference_source.database.fields.path)
       #end if
+
       blat 
             #if $noHead == "yes"
-            -noHead
+                -noHead
             #end if
+
             -q=$query_type
             -t=$database_type
+
             #if $mask_type.mask == "file.out":
-                  -mask=$mask_type.mask_file
+                  -mask='${mask_type.mask_file}'
             #else:
                   -mask=$mask_type.mask
             #end if
+
             '$reference_fasta_filename'
             '${query}'
+
             output
       && sort -k 10,10 -k 12,12n output > '${output_sorted}'
 ]]></command>
@@ -42,10 +55,10 @@
                         </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>
@@ -160,4 +173,4 @@
             
 
                
-    
\ No newline at end of file
+    
diff -r 545bc7831814 -r dede60f744f4 test-data/all_fasta.loc
diff -r 545bc7831814 -r dede60f744f4 test-data/amaVit1_Gallus/Gallus_gallus_RefSeq.fa
diff -r 545bc7831814 -r dede60f744f4 test-data/amaVit1_Gallus/amaVit1.fa
diff -r 545bc7831814 -r dede60f744f4 test-data/amaVit1_Gallus/amaVit1_Gallus_gallus.psl
diff -r 545bc7831814 -r dede60f744f4 test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl
diff -r 545bc7831814 -r dede60f744f4 test-data/dbia3/dbia3.fa
diff -r 545bc7831814 -r dede60f744f4 test-data/dbia3/dbia3.sorted.psl
diff -r 545bc7831814 -r dede60f744f4 test-data/dbia3/dbia3_RM.out
diff -r 545bc7831814 -r dede60f744f4 test-data/dbia3/dbia3_masked.2bit
diff -r 545bc7831814 -r dede60f744f4 test-data/dbia3/dbia3_masked.sorted.psl
diff -r 545bc7831814 -r dede60f744f4 test-data/dbia3/dmel-transcript.fa
diff -r 545bc7831814 -r dede60f744f4 tool-data/all_fasta.loc.sample
diff -r 545bc7831814 -r dede60f744f4 tool_data_table_conf.xml.sample
diff -r 545bc7831814 -r dede60f744f4 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 01 16:31:08 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <!-- required tools:
-        - blat
-        - sort
-        - pslReps
-        - faPolyASizes
-        - pslCDnaFilter
-    -->
-    <package name="ucsc_tools_340_for_BLAT" version="1.0">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/package_ucsc_tools_340_for_BLAT.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>
-                </actions>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>The tools and utilities were created by the UCSC Genome Bioinformatics Group</readme>
-    </package>
-</tool_dependency>
\ No newline at end of file
diff -r 545bc7831814 -r dede60f744f4 tools/ucsc_blat/.gitignore
--- a/tools/ucsc_blat/.gitignore	Thu Jun 01 16:31:08 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-*.DS_Store
-.gitignore
-*.DS_Store
-.gitignore