def get_xml(usermod, module_name, short_name):
"""
Get the galaxy XML describing a single tool.
@param usermod: module object
@param module_name: something like '20100707a'
@param short_name: something like 'plot_pca_3d'
@return: contents of a galaxy XML interface file
"""
# get module info
form_objects = usermod.get_form()
if hasattr(usermod, 'get_form_out'):
form_out = usermod.get_form_out()
else:
raise FormOutError('snippet %s provides no output '
'format information' % module_name)
doc_lines = Util.get_stripped_lines(usermod.__doc__.splitlines())
try:
tags = usermod.g_tags
except AttributeError:
tags = []
# create the python command string with wildcards
cmd = make_command(module_name, form_objects)
# build the xml
desc_prefix, desc_suffix = galaxyutil.get_split_title(doc_lines[0])
tool = etree.Element('tool',
id=short_name,
name=desc_prefix,
version='1.0.0')
if desc_suffix:
etree.SubElement(tool, 'description').text = desc_suffix
etree.SubElement(tool, 'command', interpreter='python').text = cmd
inputs = etree.SubElement(tool, 'inputs')
outputs = etree.SubElement(tool, 'outputs')
# add inputs
for obj in form_objects:
if not obj.web_only():
obj.add_galaxy_xml(inputs)
# add output
etree.SubElement(outputs,
'data',
format=form_out.get_galaxy_format(),
name='out_file1')
# Add the format tweak if there is an image.
# This is a hack required because galaxy does not
# play well with apps which have varying output formats.
# See the EMBOSS apps for more examples.
if 'imageformat' in [x.label for x in form_objects]:
etree.SubElement(tool, 'code', file='galaxy_format_tweak.py')
# serialize the xml
return etree.tostring(etree.ElementTree(tool), pretty_print=True)
def get_xml(usermod, module_name, short_name):
"""
Get the galaxy XML describing a single tool.
@param usermod: module object
@param module_name: something like '20100707a'
@param short_name: something like 'plot_pca_3d'
@return: contents of a galaxy XML interface file
"""
# get module info
form_objects = usermod.get_form()
if hasattr(usermod, 'get_form_out'):
form_out = usermod.get_form_out()
else:
raise FormOutError(
'snippet %s provides no output '
'format information' % module_name)
doc_lines = Util.get_stripped_lines(usermod.__doc__.splitlines())
try:
tags = usermod.g_tags
except AttributeError:
tags = []
# create the python command string with wildcards
cmd = make_command(module_name, form_objects)
# build the xml
desc_prefix, desc_suffix = galaxyutil.get_split_title(doc_lines[0])
tool = etree.Element('tool',
id=short_name, name=desc_prefix, version='1.0.0')
if desc_suffix:
etree.SubElement(tool, 'description').text = desc_suffix
etree.SubElement(tool, 'command', interpreter='python').text = cmd
inputs = etree.SubElement(tool, 'inputs')
outputs = etree.SubElement(tool, 'outputs')
# add inputs
for obj in form_objects:
if not obj.web_only():
obj.add_galaxy_xml(inputs)
# add output
etree.SubElement(outputs, 'data',
format=form_out.get_galaxy_format(),
name='out_file1')
# Add the format tweak if there is an image.
# This is a hack required because galaxy does not
# play well with apps which have varying output formats.
# See the EMBOSS apps for more examples.
if 'imageformat' in [x.label for x in form_objects]:
etree.SubElement(tool, 'code', file='galaxy_format_tweak.py')
# serialize the xml
return etree.tostring(etree.ElementTree(tool), pretty_print=True)
def get_suite_config_xml(added_infos, suite_name):
"""
Create suite_config.xml contents for a galaxy tool suite archive.
@param added_infos: ImportedModuleInfo objects for added tools
@param suite_name: the name of the suite directory, not the whole path
@return: contents of suite_config.xml
"""
suite = etree.Element('suite', id=suite_name,
name='Suite of misc tools', version='1.0.0')
suite_description = 'Suite of misc tools for Galaxy'
etree.SubElement(suite, 'description').text = suite_description
for info in added_infos:
module_id = info.get_identifier()
module_name = galaxyutil.get_split_title(info.get_title())[0]
module_description = info.get_title()
tool = etree.SubElement(suite, 'tool',
id=module_id, name=module_name, version='1.0.0')
etree.SubElement(tool, 'description').text = module_description
return etree.tostring(etree.ElementTree(suite), pretty_print=True)
def get_suite_config_xml(added_infos, suite_name):
"""
Create suite_config.xml contents for a galaxy tool suite archive.
@param added_infos: ImportedModuleInfo objects for added tools
@param suite_name: the name of the suite directory, not the whole path
@return: contents of suite_config.xml
"""
suite = etree.Element('suite',
id=suite_name,
name='Suite of misc tools',
version='1.0.0')
suite_description = 'Suite of misc tools for Galaxy'
etree.SubElement(suite, 'description').text = suite_description
for info in added_infos:
module_id = info.get_identifier()
module_name = galaxyutil.get_split_title(info.get_title())[0]
module_description = info.get_title()
tool = etree.SubElement(suite,
'tool',
id=module_id,
name=module_name,
version='1.0.0')
etree.SubElement(tool, 'description').text = module_description
return etree.tostring(etree.ElementTree(suite), pretty_print=True)
