Added additional options to the liftOver tool. It now supports GFF and GTF formats and allows multiple output regions and related options.

tools/extract/liftOver_wrapper.py

@@ -34,15 +34,27 @@ def safe_bed_file(infile):
     out_handle.close()
     return fname
     
-if len( sys.argv ) != 7:
-    stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey minMatch" )
+if len( sys.argv ) < 9:
+    stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey infile_type minMatch multiple <minChainT> <minChainQ> <minSizeQ>" )
 
 infile = sys.argv[1]
 outfile1 = sys.argv[2]
 outfile2 = sys.argv[3]
 in_dbkey = sys.argv[4]
 mapfilepath = sys.argv[5]
-minMatch = sys.argv[6]
+infile_type = sys.argv[6]
+gff_option = ""
+if infile_type == "gff":
+    gff_option = "-gff "
+minMatch = sys.argv[7]
+multiple = int(sys.argv[8])
+multiple_option = ""
+if multiple:
+    minChainT = sys.argv[9]
+    minChainQ = sys.argv[10]
+    minSizeQ = sys.argv[11]
+    multiple_option = " -multiple -minChainT=%s -minChainQ=%s -minSizeQ=%s " %(minChainT,minChainQ,minSizeQ)
+
 try:
     assert float(minMatch)
 except:
@@ -55,7 +67,8 @@ if not os.path.isfile( mapfilepath ):
     stop_err( "%s mapping is not currently available."  % ( mapfilepath.split('/')[-1].split('.')[0] ) )
 
 safe_infile = safe_bed_file(infile)
-cmd_line = "liftOver -minMatch=" + str(minMatch) + " " + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null"
+cmd_line = "liftOver " + gff_option + "-minMatch=" + str(minMatch) + multiple_option + " "  + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null"
+
 try:
     # have to nest try-except in try-finally to handle 2.4
     try:

tools/extract/liftOver_wrapper.xml

@@ -1,8 +1,21 @@
-<tool id="liftOver1" name="Convert genome coordinates" version="1.0.2">
+<tool id="liftOver1" name="Convert genome coordinates" version="1.0.3">
   <description> between assemblies and genomes</description>
-  <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command>
+  <command interpreter="python">
+  liftOver_wrapper.py 
+  $input 
+  "$out_file1" 
+  "$out_file2" 
+  $dbkey 
+  $to_dbkey 
+  #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__) or isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gtf').__class__):
+        "gff"
+  #else:
+        "interval"
+  #end if
+  $minMatch ${multiple.choice} ${multiple.minChainT} ${multiple.minChainQ} ${multiple.minSizeQ}
+  </command>
   <inputs>
-    <param format="interval" name="input" type="data" label="Convert coordinates of">
+    <param format="interval,gff,gtf" name="input" type="data" label="Convert coordinates of">
       <validator type="unspecified_build" />
       <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
     </param>
@@ -14,7 +27,23 @@
         <filter type="data_meta" ref="input" key="dbkey" column="0" />
       </options>
     </param> 
-    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" />
+    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" />
+    <conditional name="multiple">
+	    <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes">
+	    	<option value="0" selected="true">No</option>
+	    	<option value="1">Yes</option>
+		</param>
+		<when value="0">
+		    <param name="minSizeQ" type="hidden" value="0" />
+    		<param name="minChainQ" type="hidden" value="0" />
+    		<param name="minChainT" type="hidden" value="0" />
+    	</when>
+    	<when value="1">
+    	    <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/>
+    		<param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/>
+    		<param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
+    	</when>
+	</conditional>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" label="${tool.name} on ${on_string} [ MAPPED COORDINATES ]">
@@ -37,9 +66,40 @@
       <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
       <param name="to_dbkey" value="panTro2" />
       <param name="minMatch" value="0.95" />
+      <param name="choice" value="0" />
       <output name="out_file1" file="5_liftover_mapped.bed"/>
       <output name="out_file2" file="5_liftover_unmapped.bed"/>
     </test>
+    <test>
+      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
+      <param name="to_dbkey" value="panTro2" />
+      <param name="minMatch" value="0.10" />
+      <param name="choice" value="1" />
+      <param name="minSizeQ" value="0" />
+      <param name="minChainQ" value="500" />
+      <param name="minChainT" value="500" />
+      <output name="out_file1" file="5_mult_liftover_mapped.bed"/>
+      <output name="out_file2" file="5_mult_liftover_unmapped.bed"/>
+    </test>
+    <test>
+      <param name="input" value="cuffcompare_in1.gtf" dbkey="hg18" ftype="gtf" />
+      <param name="to_dbkey" value="panTro2" />
+      <param name="minMatch" value="0.95" />
+      <param name="choice" value="0" />
+      <output name="out_file1" file="cuffcompare_in1_liftover_mapped.bed"/>
+      <output name="out_file2" file="cuffcompare_in1_liftover_unmapped.bed"/>
+    </test>
+    <test>
+      <param name="input" value="cuffcompare_in1.gtf" dbkey="hg18" ftype="gtf" />
+      <param name="to_dbkey" value="panTro2" />
+      <param name="minMatch" value="0.10" />
+      <param name="choice" value="1" />
+      <param name="minSizeQ" value="0" />
+      <param name="minChainQ" value="500" />
+      <param name="minChainT" value="500" />
+      <output name="out_file1" file="cuffcompare_in1_mult_liftover_mapped.bed"/>
+      <output name="out_file2" file="cuffcompare_in1_mult_liftover_unmapped.bed"/>
+    </test>
   </tests>
   <help>
 .. class:: warningmark
@@ -48,7 +108,7 @@ Make sure that the genome build of the input dataset is specified (click the pen
 
 .. class:: warningmark
 
-This tool will only work on interval datasets with chromosome in column 1,
+This tool can work with interval, GFF, and GTF datasets. It requires the interval datasets to have chromosome in column 1,
 start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
 and track and browser lines will be ignored, but if other non-interval lines
 are present the tool will return empty output datasets.
@@ -59,7 +119,11 @@ are present the tool will return empty output datasets.
 
 **What it does**
 
-This tool converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any. 
+This tool is based on the LiftOver utility and Chain track from `the UC Santa Cruz Genome Browser`__.
+
+It converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any. 
+
+ .. __: http://genome.ucsc.edu/
 
 -----