mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 07:19:13 +08:00
73 lines
2.6 KiB
Python
73 lines
2.6 KiB
Python
from base.twilltestcase import TwillTestCase
|
|
#from twilltestcase import TwillTestCase
|
|
|
|
class EditModifyTests(TwillTestCase):
|
|
|
|
def test_00_first(self): # will run first due to its name
|
|
"""3D_Edit_Modify: Clearing history"""
|
|
self.clear_history()
|
|
|
|
def test_10_Encode_cds(self):
|
|
"""3D_Edit_Modify: Get Encode CDs first"""
|
|
self.clear_history()
|
|
|
|
self.run_tool('encode_import_gencode1', hg17=['gencode.CDS.20051206.bed'])
|
|
self.wait()
|
|
self.check_data('sc_3D_cds.bed', hid=1)
|
|
|
|
def test_11_Add_column_1(self):
|
|
"""3D_Edit_Modify: Add value 1 to cds"""
|
|
self.run_tool("addValue", input=1, exp="1", iterate="no")
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_add_1.bed', hid=2)
|
|
|
|
def test_12_Add_column_Mycds(self):
|
|
"""3D_Edit_Modify: Add value 'My.cds' to cds"""
|
|
self.delete_data(2)
|
|
self.run_tool("addValue", input=1, exp="My.cds", iterate="no")
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_add_mycds.bed', hid=3)
|
|
|
|
def test_21_compute1(self):
|
|
"""3D_Edit_Modify: Compute expression c3-c2"""
|
|
self.delete_data(3)
|
|
self.run_tool('Add a column1', input=1, cond='c3-c2')
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_compute1.bed', hid=4)
|
|
|
|
def test_22_compute2(self):
|
|
"""3D_Edit_Modify: Compute expression(c3-c2)*100"""
|
|
self.delete_data(4)
|
|
self.run_tool('Add a column1', input=1, cond='(c3-c2)*100')
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_compute2.bed', hid=5)
|
|
|
|
def test_30_concatenate(self):
|
|
"""3D_Edit_Modify: Concatenate cd and cds"""
|
|
self.delete_data(5)
|
|
self.run_tool('cat1', input1=1, input2=1)
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_concat.bed', hid=6)
|
|
|
|
def test_40_create_single_interval(self):
|
|
"""3D_Edit_Modify: Create single interval"""
|
|
self.delete_data(6)
|
|
self.run_tool('createInterval', chrom='chr7', start='100', end='1000', name='myInterval', strand='plus')
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_createInterval.bed', hid=7)
|
|
|
|
def test_50_cut(self):
|
|
"""3D_Edit_Modify: cut c1, c2"""
|
|
self.delete_data(7)
|
|
self.run_tool('Cut1', input=1, columnList='c1,c2', delimiter='T')
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_cut.bed', hid=8)
|
|
|
|
def test_60_paste(self):
|
|
"""3D_Edit_Modify: paste"""
|
|
self.delete_data(8)
|
|
self.run_tool('Paste1', input1=1, input2=1, delimiter='T')
|
|
self.wait()
|
|
self.check_data('sc_3D_cds_paste.bed', hid=9)
|
|
self.delete_data(9)
|