From 56032de2bd0199e9679bfb3f8de89bebfbada048 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Tue, 10 Nov 2009 13:47:34 -0500 Subject: [PATCH] Upgrade to Cheetah 2.2.2 --- eggs.ini | 4 +-- lib/galaxy/eggs/__init__.py | 1 + scripts/scramble/lib/get_platform.py | 18 ++++++++++ .../scripts/{Cheetah-py2.5.py => Cheetah.py} | 33 ++++++++++------- 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 +++++----- .../aggregate_binned_scores_in_intervals.xml | 6 ++-- 22 files changed, 109 insertions(+), 74 deletions(-) create mode 100644 scripts/scramble/lib/get_platform.py rename scripts/scramble/scripts/{Cheetah-py2.5.py => Cheetah.py} (64%) diff --git a/eggs.ini b/eggs.ini index cbcfc403e4d..00f72dd64dd 100644 --- a/eggs.ini +++ b/eggs.ini @@ -13,7 +13,7 @@ no_auto = pbs_python DRMAA_python [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 @@ GeneTrack = _dev_raa786e9fc131d998e532a1aef39d108850c9e93d ; 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.gz +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-1.2.2.tar.gz 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 --git a/lib/galaxy/eggs/__init__.py b/lib/galaxy/eggs/__init__.py index aade74a8233..cd4fb1bffc0 100644 --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -140,6 +140,7 @@ class Egg( object ): 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 --git a/scripts/scramble/lib/get_platform.py b/scripts/scramble/lib/get_platform.py new file mode 100644 index 00000000000..3a6775fa2b1 --- /dev/null +++ b/scripts/scramble/lib/get_platform.py @@ -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 --git a/scripts/scramble/scripts/Cheetah-py2.5.py b/scripts/scramble/scripts/Cheetah.py similarity index 64% rename from scripts/scramble/scripts/Cheetah-py2.5.py rename to scripts/scramble/scripts/Cheetah.py index c6d05867006..3aae6001511 100644 --- a/scripts/scramble/scripts/Cheetah-py2.5.py +++ b/scripts/scramble/scripts/Cheetah.py @@ -7,6 +7,7 @@ if 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 * @@ -25,20 +26,26 @@ for dir in [ "build", "dist" ]: 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 +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() + i.close() + o.close() # reset args for distutils me = sys.argv[0] diff --git a/scripts/scramble/scripts/DRMAA_python.py b/scripts/scramble/scripts/DRMAA_python.py index e55155f8b61..d064027ffa6 100644 --- a/scripts/scramble/scripts/DRMAA_python.py +++ b/scripts/scramble/scripts/DRMAA_python.py @@ -12,6 +12,7 @@ if 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 try: from setuptools import * import pkg_resources diff --git a/scripts/scramble/scripts/MySQL_python.py b/scripts/scramble/scripts/MySQL_python.py index 0b980071dd3..f015e92f15f 100644 --- a/scripts/scramble/scripts/MySQL_python.py +++ b/scripts/scramble/scripts/MySQL_python.py @@ -57,6 +57,7 @@ if 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 * diff --git a/scripts/scramble/scripts/generic.py b/scripts/scramble/scripts/generic.py index e79746b9d17..5e00e8d333b 100644 --- a/scripts/scramble/scripts/generic.py +++ b/scripts/scramble/scripts/generic.py @@ -7,6 +7,7 @@ if 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 * diff --git a/scripts/scramble/scripts/pbs_python.py b/scripts/scramble/scripts/pbs_python.py index 6c898642564..65cb0933240 100644 --- a/scripts/scramble/scripts/pbs_python.py +++ b/scripts/scramble/scripts/pbs_python.py @@ -12,6 +12,7 @@ if 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 try: from setuptools import * import pkg_resources diff --git a/scripts/scramble/scripts/psycopg2.py b/scripts/scramble/scripts/psycopg2.py index 1fdb2bbca59..989538fb34b 100644 --- a/scripts/scramble/scripts/psycopg2.py +++ b/scripts/scramble/scripts/psycopg2.py @@ -59,6 +59,7 @@ if 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 try: from setuptools import * import pkg_resources diff --git a/scripts/scramble/scripts/pysqlite.py b/scripts/scramble/scripts/pysqlite.py index 608af44ae5b..0c97eee5256 100644 --- a/scripts/scramble/scripts/pysqlite.py +++ b/scripts/scramble/scripts/pysqlite.py @@ -21,6 +21,7 @@ if 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 try: from setuptools import * import pkg_resources diff --git a/scripts/scramble/scripts/python_lzo.py b/scripts/scramble/scripts/python_lzo.py index 0d015f6f3b3..28d8b186754 100644 --- a/scripts/scramble/scripts/python_lzo.py +++ b/scripts/scramble/scripts/python_lzo.py @@ -54,6 +54,7 @@ if 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 try: from setuptools import * import pkg_resources diff --git a/tools/filters/joiner.xml b/tools/filters/joiner.xml index 1e455e76a7b..1a821ec908e 100644 --- a/tools/filters/joiner.xml +++ b/tools/filters/joiner.xml @@ -52,24 +52,25 @@ <% 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 )} diff --git a/tools/maf/genebed_maf_to_fasta.xml b/tools/maf/genebed_maf_to_fasta.xml index ea209878646..d926aca3e38 100644 --- a/tools/maf/genebed_maf_to_fasta.xml +++ b/tools/maf/genebed_maf_to_fasta.xml @@ -1,8 +1,9 @@ given a set of coding exon intervals - #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 + + #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 diff --git a/tools/maf/interval2maf.xml b/tools/maf/interval2maf.xml index ed8f97c9368..f3e0f69dd48 100644 --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -1,11 +1,11 @@ given a set of genomic intervals - #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 diff --git a/tools/maf/interval_maf_to_merged_fasta.xml b/tools/maf/interval_maf_to_merged_fasta.xml index fbb41363b17..5457717aeb3 100644 --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -1,8 +1,9 @@ given a set of genomic intervals - #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 + + #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 diff --git a/tools/maf/maf_to_fasta.xml b/tools/maf/maf_to_fasta.xml index 056c4afb710..462164eb565 100644 --- a/tools/maf/maf_to_fasta.xml +++ b/tools/maf/maf_to_fasta.xml @@ -1,9 +1,9 @@ Converts a MAF formated file to FASTA format - #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# diff --git a/tools/metag_tools/blat_wrapper.xml b/tools/metag_tools/blat_wrapper.xml index 2da6827ab03..f018f1a7b39 100644 --- a/tools/metag_tools/blat_wrapper.xml +++ b/tools/metag_tools/blat_wrapper.xml @@ -1,10 +1,9 @@ compare sequencing reads against UCSC genome builds - #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} diff --git a/tools/metag_tools/shrimp_color_wrapper.xml b/tools/metag_tools/shrimp_color_wrapper.xml index a564ece2a02..428431ff350 100644 --- a/tools/metag_tools/shrimp_color_wrapper.xml +++ b/tools/metag_tools/shrimp_color_wrapper.xml @@ -1,9 +1,9 @@ reads mapping against reference sequence - #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 $param.sw_vector_hit_threshold + #end if# diff --git a/tools/metag_tools/shrimp_wrapper.xml b/tools/metag_tools/shrimp_wrapper.xml index 0d400315fec..f411cde3877 100644 --- a/tools/metag_tools/shrimp_wrapper.xml +++ b/tools/metag_tools/shrimp_wrapper.xml @@ -1,11 +1,11 @@ reads mapping against reference sequence - #if ($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# diff --git a/tools/samtools/pileup_parser.xml b/tools/samtools/pileup_parser.xml index 571d3750a0e..8a7ee9bf4f6 100644 --- a/tools/samtools/pileup_parser.xml +++ b/tools/samtools/pileup_parser.xml @@ -1,10 +1,10 @@ on coverage and SNPs - #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 $out_file1 + #end if# diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml index 4efba932afd..ffb5eea2be2 100644 --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -1,15 +1,15 @@ map short reads against reference sequence - #if ($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# diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml index 140540ab148..8a0bc9147ed 100644 --- a/tools/stats/aggregate_binned_scores_in_intervals.xml +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml @@ -1,9 +1,9 @@ Appends the average, min, max of datapoints per interval - #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#