mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Upgrade to Cheetah 2.2.2
This commit is contained in:
Nate Coraor
@@ -13,7 +13,7 @@ no_auto = pbs_python DRMAA_python
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[eggs:platform]
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bx_python = 0.5.0
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Cheetah = 1.0
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Cheetah = 2.2.2
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DRMAA_python = 0.2
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MySQL_python = 1.2.2
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pbs_python = 2.9.4
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@@ -66,7 +66,7 @@ GeneTrack = _dev_raa786e9fc131d998e532a1aef39d108850c9e93d
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; source location, necessary for scrambling
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[source]
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bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2
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Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz
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Cheetah = http://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.2.2.tar.gz
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DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz
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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
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pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz
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@@ -140,6 +140,7 @@ class Egg( object ):
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cmd = "ssh %s 'cd %s; %s -ES %s'" % ( self.build_host, self.buildpath, self.python, "scramble.py" )
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else:
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cmd = "%s -ES %s" % ( self.python, "scramble.py" )
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log.debug( 'Executing: %s' % cmd )
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p = subprocess.Popen( args = cmd, shell = True, cwd = self.buildpath )
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r = p.wait()
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if r != 0:
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@@ -0,0 +1,18 @@
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"""
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Monkeypatch get_platform since it's broken on OS X versions of Python 2.5
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"""
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import os, sys
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from distutils.sysconfig import get_config_vars
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if sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip():
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# Has to be before anything imports pkg_resources
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def _get_platform_monkeypatch():
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plat = distutils.util._get_platform()
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if plat.startswith( 'macosx-' ):
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plat = 'macosx-10.3-fat'
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return plat
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import distutils.util
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try:
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assert distutils.util._get_platform
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except:
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distutils.util._get_platform = distutils.util.get_platform
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distutils.util.get_platform = _get_platform_monkeypatch
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@@ -7,6 +7,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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from ez_setup import use_setuptools
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use_setuptools( download_delay=8, to_dir=scramble_lib )
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from setuptools import *
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@@ -25,20 +26,26 @@ for dir in [ "build", "dist" ]:
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shutil.rmtree( dir )
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# patch
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for file in [ "src/NameMapper.py", "src/Tests/NameMapper.py" ]:
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if not os.access( "%s.orig" %file, os.F_OK ):
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print "scramble_it(): Patching", file
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shutil.copyfile( file, "%s.orig" %file )
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i = open( "%s.orig" %file, "r" )
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o = open( file, "w" )
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for line in i.readlines():
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if line.startswith("__author__ ="):
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print >>o, "from __future__ import generators"
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elif line == "from __future__ import generators\n":
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continue
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file = "SetupConfig.py"
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if not os.access( "%s.orig" %file, os.F_OK ):
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print "scramble.py(): Patching", file
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shutil.copyfile( file, "%s.orig" %file )
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i = open( "%s.orig" %file, "r" )
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o = open( file, "w" )
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comment = False
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for line in i.readlines():
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if line == " install_requires = [\n":
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comment = True
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print >>o, "#" + line,
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elif comment and line == " ]\n":
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comment = False
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print >>o, "#" + line,
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elif comment:
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print >>o, "#" + line,
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else:
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print >>o, line,
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i.close()
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o.close()
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i.close()
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o.close()
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# reset args for distutils
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me = sys.argv[0]
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@@ -12,6 +12,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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try:
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from setuptools import *
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import pkg_resources
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@@ -57,6 +57,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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from ez_setup import use_setuptools
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use_setuptools( download_delay=8, to_dir=scramble_lib )
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from setuptools import *
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@@ -7,6 +7,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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from ez_setup import use_setuptools
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use_setuptools( download_delay=8, to_dir=scramble_lib )
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from setuptools import *
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@@ -12,6 +12,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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try:
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from setuptools import *
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import pkg_resources
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@@ -59,6 +59,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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try:
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from setuptools import *
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import pkg_resources
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@@ -21,6 +21,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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try:
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from setuptools import *
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import pkg_resources
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@@ -54,6 +54,7 @@ if os.path.dirname( sys.argv[0] ) != "":
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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import get_platform # fixes fat python 2.5
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try:
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from setuptools import *
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import pkg_resources
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+18
-17
@@ -52,24 +52,25 @@
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<configfiles>
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<configfile name="fill_options_file"><%
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import simplejson
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%>#set $__fill_options = {}
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%>
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#set $__fill_options = {}
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#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
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#set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only'
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#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value':
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#set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value
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#else:
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#set $__start_fill = ""
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#end if
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#set $__fill_options['file1_columns'] = [ $__start_fill for i in range( int( $input1.metadata.columns ) ) ]
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#set $__fill_options['file2_columns'] = [ $__start_fill for i in range( int( $input2.metadata.columns ) ) ]
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#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column':
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#for column_fill1 in $fill_empty_columns['do_fill_empty_columns']['column_fill1']:
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#set $__fill_options['file1_columns'][ int( column_fill1['column_number1'].value ) - 1 ] = column_fill1['fill_value1'].value
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#end for
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#for column_fill2 in $fill_empty_columns['do_fill_empty_columns']['column_fill2']:
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#set $__fill_options['file2_columns'][ int( column_fill2['column_number2'].value ) - 1 ] = column_fill2['fill_value2'].value
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#end for
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#end if
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#set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only'
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#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value':
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#set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value
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#else:
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#set $__start_fill = ""
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#end if
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#set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ]
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#set $__fill_options['file2_columns'] = [ __start_fill for i in range( int( $input2.metadata.columns ) ) ]
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#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column':
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#for column_fill1 in $fill_empty_columns['do_fill_empty_columns']['column_fill1']:
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#set $__fill_options['file1_columns'][ int( column_fill1['column_number1'].value ) - 1 ] = column_fill1['fill_value1'].value
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#end for
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#for column_fill2 in $fill_empty_columns['do_fill_empty_columns']['column_fill2']:
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#set $__fill_options['file2_columns'][ int( column_fill2['column_number2'].value ) - 1 ] = column_fill2['fill_value2'].value
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#end for
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#end if
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#end if
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${simplejson.dumps( __fill_options )}
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</configfile>
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@@ -1,8 +1,9 @@
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<tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks" version="1.0.1">
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<description>given a set of coding exon intervals</description>
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<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=${GALAXY_DATA_INDEX_DIR}
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#else:#interval_maf_to_merged_fasta.py --dbkey=$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}
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#end if# --overwrite_with_gaps=$overwrite_with_gaps
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<command interpreter="python">
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#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=${GALAXY_DATA_INDEX_DIR}
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#else #interval_maf_to_merged_fasta.py --dbkey=$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}
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#end if# --overwrite_with_gaps=$overwrite_with_gaps
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</command>
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<inputs>
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<param name="input1" type="data" format="bed" label="Gene BED File">
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@@ -1,11 +1,11 @@
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<tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1">
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<description>given a set of genomic intervals</description>
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<command interpreter="python">
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#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
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#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
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#end if
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--split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species
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#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
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#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
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#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
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#end if# --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species
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#if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"#
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--remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns
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#end if
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</command>
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<inputs>
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@@ -1,8 +1,9 @@
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<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1">
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<description>given a set of genomic intervals</description>
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<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=${GALAXY_DATA_INDEX_DIR}
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#else:#interval_maf_to_merged_fasta.py --dbkey=$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}
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#end if# --overwrite_with_gaps=$overwrite_with_gaps
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<command interpreter="python">
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#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=${GALAXY_DATA_INDEX_DIR}
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#else #interval_maf_to_merged_fasta.py --dbkey=$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}
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#end if# --overwrite_with_gaps=$overwrite_with_gaps
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</command>
|
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<inputs>
|
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<page>
|
||||
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@@ -1,9 +1,9 @@
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<tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1">
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<description>Converts a MAF formated file to FASTA format</description>
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<command interpreter="python">
|
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#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
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#else:#maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1
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#end if
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#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
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#else #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1
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#end if#
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</command>
|
||||
<inputs>
|
||||
<param format="maf" name="input1" type="data" label="MAF file to convert"/>
|
||||
|
||||
@@ -1,10 +1,9 @@
|
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<tool id="blat_wrapper" name="BLAT" version="1.0.0">
|
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<description> compare sequencing reads against UCSC genome builds</description>
|
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<command interpreter="python">
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#if $source.source_select=="database":#blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
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#else:#blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
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#end if
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${GALAXY_DATA_INDEX_DIR}
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#if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
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#else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
|
||||
#end if# ${GALAXY_DATA_INDEX_DIR}
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</command>
|
||||
<inputs>
|
||||
<conditional name="source">
|
||||
|
||||
@@ -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 $param.sw_vector_hit_threshold
|
||||
#end if#
|
||||
</command>
|
||||
<inputs>
|
||||
<page>
|
||||
|
||||
@@ -1,11 +1,11 @@
|
||||
<tool id="shrimp_wrapper" name="SHRiMP for Letter-space" version="1.0.0">
|
||||
<description>reads mapping against reference sequence </description>
|
||||
<command interpreter="python">
|
||||
#if ($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>
|
||||
|
||||
@@ -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 $out_file1
|
||||
#end if#
|
||||
</command>
|
||||
<inputs>
|
||||
<param name="input" type="data" format="tabular" label="Select dataset"/>
|
||||
|
||||
@@ -1,15 +1,15 @@
|
||||
<tool id="lastz_wrapper_1" name="Lastz" version="1.0.0">
|
||||
<description> map short reads against reference sequence</description>
|
||||
<command>
|
||||
#if ($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" />
|
||||
|
||||
@@ -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">
|
||||
|
||||
Reference in New Issue
Block a user