1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/d306dfb77ea3/ changeset: d306dfb77ea3 user: guru date: 2011-07-26 22:14:31 summary: Added additional options to the liftOver tool. It now supports GFF and GTF formats and allows multiple output regions and related options. affected #: 8 files (3.4 KB)

--- a/tools/extract/liftOver_wrapper.py Tue Jul 26 13:30:07 2011 -0400 +++ b/tools/extract/liftOver_wrapper.py Tue Jul 26 16:14:31 2011 -0400 @@ -34,15 +34,27 @@ 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 @@ 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:

--- a/tools/extract/liftOver_wrapper.xml Tue Jul 26 13:30:07 2011 -0400 +++ b/tools/extract/liftOver_wrapper.xml Tue Jul 26 16:14:31 2011 -0400 @@ -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 @@

.. 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 @@

**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/

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Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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