details: http://www.bx.psu.edu/hg/galaxy/rev/c146726d274f changeset: 3001:c146726d274f user: Nate Coraor <nate@bx.psu.edu> date: Tue Nov 10 13:47:34 2009 -0500 description: Upgrade to Cheetah 2.2.2 diffstat: eggs.ini | 4 +- lib/galaxy/eggs/__init__.py | 1 + scripts/scramble/lib/get_platform.py | 18 ++++++ scripts/scramble/scripts/Cheetah-py2.5.py | 55 ------------------ scripts/scramble/scripts/Cheetah.py | 62 ++++++++++++++++++++ scripts/scramble/scripts/DRMAA_python.py | 1 + scripts/scramble/scripts/MySQL_python.py | 1 + scripts/scramble/scripts/generic.py | 1 + scripts/scramble/scripts/pbs_python.py | 1 + scripts/scramble/scripts/psycopg2.py | 1 + scripts/scramble/scripts/pysqlite.py | 1 + scripts/scramble/scripts/python_lzo.py | 1 + tools/filters/joiner.xml | 35 ++++++----- tools/maf/genebed_maf_to_fasta.xml | 7 +- tools/maf/interval2maf.xml | 10 +- tools/maf/interval_maf_to_merged_fasta.xml | 7 +- tools/maf/maf_to_fasta.xml | 6 +- tools/metag_tools/blat_wrapper.xml | 7 +- tools/metag_tools/shrimp_color_wrapper.xml | 6 +- tools/metag_tools/shrimp_wrapper.xml | 10 +- tools/samtools/pileup_parser.xml | 8 +- tools/sr_mapping/lastz_wrapper.xml | 18 +++--- tools/stats/aggregate_binned_scores_in_intervals.xml | 6 +- 23 files changed, 151 insertions(+), 116 deletions(-) diffs (485 lines): diff -r facf315d9e0e -r c146726d274f eggs.ini --- a/eggs.ini Tue Nov 10 13:46:53 2009 -0500 +++ b/eggs.ini Tue Nov 10 13:47:34 2009 -0500 @@ -13,7 +13,7 @@ [eggs:platform] bx_python = 0.5.0 -Cheetah = 1.0 +Cheetah = 2.2.2 DRMAA_python = 0.2 MySQL_python = 1.2.2 pbs_python = 2.9.4 @@ -66,7 +66,7 @@ ; source location, necessary for scrambling [source] bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 -Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.... +Cheetah = http://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.2.2.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python-... http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz diff -r facf315d9e0e -r c146726d274f lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Tue Nov 10 13:46:53 2009 -0500 +++ b/lib/galaxy/eggs/__init__.py Tue Nov 10 13:47:34 2009 -0500 @@ -140,6 +140,7 @@ cmd = "ssh %s 'cd %s; %s -ES %s'" % ( self.build_host, self.buildpath, self.python, "scramble.py" ) else: cmd = "%s -ES %s" % ( self.python, "scramble.py" ) + log.debug( 'Executing: %s' % cmd ) p = subprocess.Popen( args = cmd, shell = True, cwd = self.buildpath ) r = p.wait() if r != 0: diff -r facf315d9e0e -r c146726d274f scripts/scramble/lib/get_platform.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/lib/get_platform.py Tue Nov 10 13:47:34 2009 -0500 @@ -0,0 +1,18 @@ +""" +Monkeypatch get_platform since it's broken on OS X versions of Python 2.5 +""" +import os, sys +from distutils.sysconfig import get_config_vars +if sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip(): + # Has to be before anything imports pkg_resources + def _get_platform_monkeypatch(): + plat = distutils.util._get_platform() + if plat.startswith( 'macosx-' ): + plat = 'macosx-10.3-fat' + return plat + import distutils.util + try: + assert distutils.util._get_platform + except: + distutils.util._get_platform = distutils.util.get_platform + distutils.util.get_platform = _get_platform_monkeypatch diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/Cheetah-py2.5.py --- a/scripts/scramble/scripts/Cheetah-py2.5.py Tue Nov 10 13:46:53 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -import os, sys, shutil - -# change back to the build dir -if os.path.dirname( sys.argv[0] ) != "": - os.chdir( os.path.dirname( sys.argv[0] ) ) - -# find setuptools -scramble_lib = os.path.join( "..", "..", "..", "lib" ) -sys.path.append( scramble_lib ) -from ez_setup import use_setuptools -use_setuptools( download_delay=8, to_dir=scramble_lib ) -from setuptools import * - -# get the tag -if os.access( ".galaxy_tag", os.F_OK ): - tagfile = open( ".galaxy_tag", "r" ) - tag = tagfile.readline().strip() -else: - tag = None - -# in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist" ]: - if os.access( dir, os.F_OK ): - print "scramble_it.py: removing dir:", dir - shutil.rmtree( dir ) - -# patch -for file in [ "src/NameMapper.py", "src/Tests/NameMapper.py" ]: - if not os.access( "%s.orig" %file, os.F_OK ): - print "scramble_it(): Patching", file - shutil.copyfile( file, "%s.orig" %file ) - i = open( "%s.orig" %file, "r" ) - o = open( file, "w" ) - for line in i.readlines(): - if line.startswith("__author__ ="): - print >>o, "from __future__ import generators" - elif line == "from __future__ import generators\n": - continue - print >>o, line, - i.close() - o.close() - -# reset args for distutils -me = sys.argv[0] -sys.argv = [ me ] -sys.argv.append( "egg_info" ) -if tag is not None: - #sys.argv.append( "egg_info" ) - sys.argv.append( "--tag-build=%s" %tag ) -# svn revision (if any) is handled directly in tag-build -sys.argv.append( "--no-svn-revision" ) -sys.argv.append( "bdist_egg" ) - -# do it -execfile( "setup.py", globals(), locals() ) diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/Cheetah.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/Cheetah.py Tue Nov 10 13:47:34 2009 -0500 @@ -0,0 +1,62 @@ +import os, sys, shutil + +# change back to the build dir +if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + +# find setuptools +scramble_lib = os.path.join( "..", "..", "..", "lib" ) +sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 +from ez_setup import use_setuptools +use_setuptools( download_delay=8, to_dir=scramble_lib ) +from setuptools import * + +# get the tag +if os.access( ".galaxy_tag", os.F_OK ): + tagfile = open( ".galaxy_tag", "r" ) + tag = tagfile.readline().strip() +else: + tag = None + +# in case you're running this by hand from a dirty module source dir +for dir in [ "build", "dist" ]: + if os.access( dir, os.F_OK ): + print "scramble_it.py: removing dir:", dir + shutil.rmtree( dir ) + +# patch +file = "SetupConfig.py" +if not os.access( "%s.orig" %file, os.F_OK ): + print "scramble.py(): Patching", file + shutil.copyfile( file, "%s.orig" %file ) + i = open( "%s.orig" %file, "r" ) + o = open( file, "w" ) + comment = False + for line in i.readlines(): + if line == " install_requires = [\n": + comment = True + print >>o, "#" + line, + elif comment and line == " ]\n": + comment = False + print >>o, "#" + line, + elif comment: + print >>o, "#" + line, + else: + print >>o, line, + i.close() + o.close() + +# reset args for distutils +me = sys.argv[0] +sys.argv = [ me ] +sys.argv.append( "egg_info" ) +if tag is not None: + #sys.argv.append( "egg_info" ) + sys.argv.append( "--tag-build=%s" %tag ) +# svn revision (if any) is handled directly in tag-build +sys.argv.append( "--no-svn-revision" ) +sys.argv.append( "bdist_egg" ) + +# do it +execfile( "setup.py", globals(), locals() ) diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/DRMAA_python.py --- a/scripts/scramble/scripts/DRMAA_python.py Tue Nov 10 13:46:53 2009 -0500 +++ b/scripts/scramble/scripts/DRMAA_python.py Tue Nov 10 13:47:34 2009 -0500 @@ -12,6 +12,7 @@ # find setuptools scramble_lib = os.path.join( "..", "..", "..", "lib" ) sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 try: from setuptools import * import pkg_resources diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/MySQL_python.py --- a/scripts/scramble/scripts/MySQL_python.py Tue Nov 10 13:46:53 2009 -0500 +++ b/scripts/scramble/scripts/MySQL_python.py Tue Nov 10 13:47:34 2009 -0500 @@ -57,6 +57,7 @@ # find setuptools scramble_lib = os.path.join( "..", "..", "..", "lib" ) sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 from ez_setup import use_setuptools use_setuptools( download_delay=8, to_dir=scramble_lib ) from setuptools import * diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/generic.py --- a/scripts/scramble/scripts/generic.py Tue Nov 10 13:46:53 2009 -0500 +++ b/scripts/scramble/scripts/generic.py Tue Nov 10 13:47:34 2009 -0500 @@ -7,6 +7,7 @@ # find setuptools scramble_lib = os.path.join( "..", "..", "..", "lib" ) sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 from ez_setup import use_setuptools use_setuptools( download_delay=8, to_dir=scramble_lib ) from setuptools import * diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Tue Nov 10 13:46:53 2009 -0500 +++ b/scripts/scramble/scripts/pbs_python.py Tue Nov 10 13:47:34 2009 -0500 @@ -12,6 +12,7 @@ # find setuptools scramble_lib = os.path.join( "..", "..", "..", "lib" ) sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 try: from setuptools import * import pkg_resources diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/psycopg2.py --- a/scripts/scramble/scripts/psycopg2.py Tue Nov 10 13:46:53 2009 -0500 +++ b/scripts/scramble/scripts/psycopg2.py Tue Nov 10 13:47:34 2009 -0500 @@ -59,6 +59,7 @@ # find setuptools scramble_lib = os.path.join( "..", "..", "..", "lib" ) sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 try: from setuptools import * import pkg_resources diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/pysqlite.py --- a/scripts/scramble/scripts/pysqlite.py Tue Nov 10 13:46:53 2009 -0500 +++ b/scripts/scramble/scripts/pysqlite.py Tue Nov 10 13:47:34 2009 -0500 @@ -21,6 +21,7 @@ # find setuptools scramble_lib = os.path.join( "..", "..", "..", "lib" ) sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 try: from setuptools import * import pkg_resources diff -r facf315d9e0e -r c146726d274f scripts/scramble/scripts/python_lzo.py --- a/scripts/scramble/scripts/python_lzo.py Tue Nov 10 13:46:53 2009 -0500 +++ b/scripts/scramble/scripts/python_lzo.py Tue Nov 10 13:47:34 2009 -0500 @@ -54,6 +54,7 @@ # find setuptools scramble_lib = os.path.join( "..", "..", "..", "lib" ) sys.path.append( scramble_lib ) +import get_platform # fixes fat python 2.5 try: from setuptools import * import pkg_resources diff -r facf315d9e0e -r c146726d274f tools/filters/joiner.xml --- a/tools/filters/joiner.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/filters/joiner.xml Tue Nov 10 13:47:34 2009 -0500 @@ -52,24 +52,25 @@ <configfiles> <configfile name="fill_options_file"><% import simplejson -%>#set $__fill_options = {} +%> +#set $__fill_options = {} #if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty': -#set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only' -#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value': -#set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value -#else: -#set $__start_fill = "" -#end if -#set $__fill_options['file1_columns'] = [ $__start_fill for i in range( int( $input1.metadata.columns ) ) ] -#set $__fill_options['file2_columns'] = [ $__start_fill for i in range( int( $input2.metadata.columns ) ) ] -#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column': -#for column_fill1 in $fill_empty_columns['do_fill_empty_columns']['column_fill1']: -#set $__fill_options['file1_columns'][ int( column_fill1['column_number1'].value ) - 1 ] = column_fill1['fill_value1'].value -#end for -#for column_fill2 in $fill_empty_columns['do_fill_empty_columns']['column_fill2']: -#set $__fill_options['file2_columns'][ int( column_fill2['column_number2'].value ) - 1 ] = column_fill2['fill_value2'].value -#end for -#end if + #set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only' + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value': + #set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value + #else: + #set $__start_fill = "" + #end if + #set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ] + #set $__fill_options['file2_columns'] = [ __start_fill for i in range( int( $input2.metadata.columns ) ) ] + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column': + #for column_fill1 in $fill_empty_columns['do_fill_empty_columns']['column_fill1']: + #set $__fill_options['file1_columns'][ int( column_fill1['column_number1'].value ) - 1 ] = column_fill1['fill_value1'].value + #end for + #for column_fill2 in $fill_empty_columns['do_fill_empty_columns']['column_fill2']: + #set $__fill_options['file2_columns'][ int( column_fill2['column_number2'].value ) - 1 ] = column_fill2['fill_value2'].value + #end for + #end if #end if ${simplejson.dumps( __fill_options )} </configfile> diff -r facf315d9e0e -r c146726d274f tools/maf/genebed_maf_to_fasta.xml --- a/tools/maf/genebed_maf_to_fasta.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/maf/genebed_maf_to_fasta.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,8 +1,9 @@ <tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks" version="1.0.1"> <description>given a set of coding exon intervals</description> - <command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} -#else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} -#end if# --overwrite_with_gaps=$overwrite_with_gaps + <command interpreter="python"> + #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} + #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} + #end if# --overwrite_with_gaps=$overwrite_with_gaps </command> <inputs> <param name="input1" type="data" format="bed" label="Gene BED File"> diff -r facf315d9e0e -r c146726d274f tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/maf/interval2maf.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,11 +1,11 @@ <tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1"> <description>given a set of genomic intervals</description> <command interpreter="python"> - #if $maf_source_type.maf_source == "user":#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species - #else:#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species - #end if - --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species - #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species":# --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns + #if $maf_source_type.maf_source == "user" #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species + #else #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species + #end if# --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species + #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"# + --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns #end if </command> <inputs> diff -r facf315d9e0e -r c146726d274f tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,8 +1,9 @@ <tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1"> <description>given a set of genomic intervals</description> - <command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} -#else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} -#end if# --overwrite_with_gaps=$overwrite_with_gaps + <command interpreter="python"> + #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} + #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} + #end if# --overwrite_with_gaps=$overwrite_with_gaps </command> <inputs> <page> diff -r facf315d9e0e -r c146726d274f tools/maf/maf_to_fasta.xml --- a/tools/maf/maf_to_fasta.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/maf/maf_to_fasta.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,9 +1,9 @@ <tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1"> <description>Converts a MAF formated file to FASTA format</description> <command interpreter="python"> - #if $fasta_target_type.fasta_type == "multiple":#maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks - #else:#maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1 - #end if + #if $fasta_target_type.fasta_type == "multiple" #maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks + #else #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1 + #end if# </command> <inputs> <param format="maf" name="input1" type="data" label="MAF file to convert"/> diff -r facf315d9e0e -r c146726d274f tools/metag_tools/blat_wrapper.xml --- a/tools/metag_tools/blat_wrapper.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/metag_tools/blat_wrapper.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,10 +1,9 @@ <tool id="blat_wrapper" name="BLAT" version="1.0.0"> <description> compare sequencing reads against UCSC genome builds</description> <command interpreter="python"> - #if $source.source_select=="database":#blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off - #else:#blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off - #end if - ${GALAXY_DATA_INDEX_DIR} + #if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off + #else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off + #end if# ${GALAXY_DATA_INDEX_DIR} </command> <inputs> <conditional name="source"> diff -r facf315d9e0e -r c146726d274f tools/metag_tools/shrimp_color_wrapper.xml --- a/tools/metag_tools/shrimp_color_wrapper.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/metag_tools/shrimp_color_wrapper.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,9 +1,9 @@ <tool id="shrimp_color_wrapper" name="SHRiMP for Color-space" version="1.0.0"> <description>reads mapping against reference sequence </description> <command interpreter="python"> - #if $param.skip_or_full=="skip":#shrimp_color_wrapper.py $input_target $input_query $output1 - #else #shrimp_color_wrapper.py $input_target $input_query $output1 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_crossover_penalty $param.sw_full_hit_threshold $param.sw_vector_hit_threshold - #end if + #if $param.skip_or_full=="skip" #shrimp_color_wrapper.py $input_target $input_query $output1 + #else #shrimp_color_wrapper.py $input_target $input_query $output1 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_crossover_penalty $param.sw_full_hit_threshold $param.sw_vector_hit_threshold + #end if# </command> <inputs> <page> diff -r facf315d9e0e -r c146726d274f tools/metag_tools/shrimp_wrapper.xml --- a/tools/metag_tools/shrimp_wrapper.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/metag_tools/shrimp_wrapper.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,11 +1,11 @@ <tool id="shrimp_wrapper" name="SHRiMP for Letter-space" version="1.0.0"> <description>reads mapping against reference sequence </description> <command interpreter="python"> - #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $input_query - #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size - #elif ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full"):#shrimp_wrapper.py $input_target $output1 $output2 $input_query $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold - #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full"):#shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold - #end if + #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip") #shrimp_wrapper.py $input_target $output1 $output2 $input_query + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip") #shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size + #elif ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full") #shrimp_wrapper.py $input_target $output1 $output2 $input_query $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full") #shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold + #end if# </command> <inputs> <page> diff -r facf315d9e0e -r c146726d274f tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/samtools/pileup_parser.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,10 +1,10 @@ <tool id="pileup_parser" name="Filter pileup"> <description>on coverage and SNPs</description> <command interpreter="perl"> - #if $pileup_type.type_select == "six": #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 - #elif $pileup_type.type_select == "ten": #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 - #elif $pileup_type.type_select == "manual": #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 - #end if + #if $pileup_type.type_select == "six" #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 + #elif $pileup_type.type_select == "ten" #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 + #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 + #end if# </command> <inputs> <param name="input" type="data" format="tabular" label="Select dataset"/> diff -r facf315d9e0e -r c146726d274f tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,15 +1,15 @@ <tool id="lastz_wrapper_1" name="Lastz" version="1.0.0"> <description> map short reads against reference sequence</description> <command> - #if ($params.source_select=="pre_set" and $seq_name.how_to_name=="No" and $out_format.value=="diffs"):#lastz $input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="Yes" and $out_format.value=="diffs"):#lastz $seq_name.ref_name::$input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #elif ($params.source_select=="full" and $seq_name.how_to_name=="No" and $out_format.value=="diffs"):#lastz $input1 ${input2}[fullnames] $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #elif ($params.source_select=="full" and $seq_name.how_to_name=="Yes" and $out_format.value=="diffs"):#lastz $seq_name.ref_name::$input1 ${input2}[fullnames] $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="No" and $out_format.value=="maf"):#lastz $input1 read::${input2} --${params.pre_set_options} --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="Yes" and $out_format.value=="maf"):#lastz $seq_name.ref_name::$input1 read::${input2} --${params.pre_set_options} --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #elif ($params.source_select=="full" and $seq_name.how_to_name=="No" and $out_format.value=="maf"):#lastz $input1 read::${input2} $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #elif ($params.source_select=="full" and $seq_name.how_to_name=="Yes" and $out_format.value=="maf"):#lastz $seq_name.ref_name::$input1 read::${input2} $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 - #end if + #if ($params.source_select=="pre_set" and $seq_name.how_to_name=="No" and $out_format.value=="diffs") #lastz $input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="Yes" and $out_format.value=="diffs") #lastz $seq_name.ref_name::$input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #elif ($params.source_select=="full" and $seq_name.how_to_name=="No" and $out_format.value=="diffs") #lastz $input1 ${input2}[fullnames] $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #elif ($params.source_select=="full" and $seq_name.how_to_name=="Yes" and $out_format.value=="diffs") #lastz $seq_name.ref_name::$input1 ${input2}[fullnames] $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="No" and $out_format.value=="maf") #lastz $input1 read::${input2} --${params.pre_set_options} --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="Yes" and $out_format.value=="maf") #lastz $seq_name.ref_name::$input1 read::${input2} --${params.pre_set_options} --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #elif ($params.source_select=="full" and $seq_name.how_to_name=="No" and $out_format.value=="maf") #lastz $input1 read::${input2} $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #elif ($params.source_select=="full" and $seq_name.how_to_name=="Yes" and $out_format.value=="maf") #lastz $seq_name.ref_name::$input1 read::${input2} $params.strand $params.seed $params.transition O=$params.O E=$params.E X=$params.X Y=$params.Y K=$params.K L=$params.L $params.entropy --ambiguousn --identity=${min_ident}..${max_ident} --census32=$output2 --coverage=$min_cvrg --format=$out_format > $output1 + #end if# </command> <inputs> <param name="input2" format="fasta" type="data" label="Align sequencing reads" /> diff -r facf315d9e0e -r c146726d274f tools/stats/aggregate_binned_scores_in_intervals.xml --- a/tools/stats/aggregate_binned_scores_in_intervals.xml Tue Nov 10 13:46:53 2009 -0500 +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml Tue Nov 10 13:47:34 2009 -0500 @@ -1,9 +1,9 @@ <tool id="aggregate_scores_in_intervals2" description="such as phastCons, GERP, binCons, and others for a set of genomic intervals" name="Aggregate datapoints" version="1.1.2"> <description>Appends the average, min, max of datapoints per interval</description> <command interpreter="python"> - #if $score_source_type.score_source == "user":#aggregate_scores_in_intervals.py $score_source_type.input2 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 --chrom_buffer=3 - #else:#aggregate_scores_in_intervals.py $score_source_type.datasets $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 -b - #end if + #if $score_source_type.score_source == "user" #aggregate_scores_in_intervals.py $score_source_type.input2 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 --chrom_buffer=3 + #else #aggregate_scores_in_intervals.py $score_source_type.datasets $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 -b + #end if# </command> <inputs> <param format="interval" name="input1" type="data" label="Interval file">