diff --git a/toolrunner.py b/toolrunner.py
deleted file mode 100644
index 453284cfbe8b27f3b2995d57dbd6b9b38f7e1123..0000000000000000000000000000000000000000
--- a/toolrunner.py
+++ /dev/null
@@ -1,153 +0,0 @@
-from bioblend import galaxy
-from bioblend.galaxy import GalaxyInstance
-import os
-"""
-Methods to run all Chado and Tripal tools on galaxy
-"""
-
-
-class ToolRunner:
-
- def __init__(self, parameters_dict, instance, history):
- self.history = history
- self.instance = instance
- self.parameters_dict = parameters_dict
- self.genus = parameters_dict["genus"]
- self.species = parameters_dict["species"]
- self.strain = parameters_dict["strain"]
- self.common = parameters_dict["common"]
- self.performed = parameters_dict["performed by"]
- self.genome_version = parameters_dict["genome version"]
- self.ogs_version = parameters_dict["ogs version"]
- self.sex = parameters_dict["sex"]
- self.date = parameters_dict["date"]
- self.custom_ga_file = None
- self.custom_ga_file_path = None
- self.preset_ga_file = None
- self.analysis = None
- self.organism = None
- self.program = None
- if self.strain != "":
- self.abbr = self.genus[0].lower() + "_" + self.species + "_" + self.strain
- self.full = "_".join([self.genus, self.species, self.strain, self.sex])
- else:
- self.abbr = self.genus[0].lower() + "_" + self.species
- self.full = "_".join([self.genus, self.species, self.strain, self.sex])
- self.ogs = str("OGS"+ self.ogs_version)
- self.genome = str(self.full + " genome v" + self.genome_version)
-
- def show_tool(self, tool_id):
- print(self.instance.tools.show_tool(tool_id=tool_id, io_details=True))
- return self.instance.tools.show_tool(tool_id=tool_id, io_details=True)
-
- def purge_organism(self):
- self.show_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2")
- self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2",
- history_id=self.history,
- tool_inputs={"name": self.organism})
-
- def purge_analyses(self):
- return None
-
- def get_organism(self):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.2",
- history_id=self.history,
- tool_inputs={"genus": self.genus, "species": self.species})
-
- def get_ogs_analysis(self):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.2",
- history_id=self.history,
- tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version})
-
- def get_genome_analysis(self):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_get_analyses/analysis_get_analyses/2.3.2",
- history_id=self.history,
- tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version})
-
- def add_organism(self):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_add_organism/organism_add_organism/2.3.2",
- history_id=self.history,
- tool_inputs={"abbr": self.abbr,
- "genus": self.genus,
- "species": self.species,
- "common": self.common
- })
-
- def add_ogs(self):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2",
- history_id=self.history,
- tool_inputs={"name": self.genus + " " + self.species + " OGS" + self.ogs_version,
- "program": "Performed by Genoscope",
- "programversion": str("OGS" + self.genome_version),
- "sourcename": "Genoscope",
- "date_executed": self.date
- })
-
- def add_genome(self):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_analysis/analysis_add_analysis/2.3.2",
- history_id=self.history,
- tool_inputs={"name": self.genus + " " + self.species + " genome v" + self.genome_version,
- "program": "Performed by Genoscope",
- "programversion": str("genome v" + self.genome_version),
- "sourcename": "Genoscope",
- "date_executed": self.date
- })
-
- def add_jbrowse(self, datasets):
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.5+galaxy7",
- history_id=self.history,
- tool_inputs={"genomes": datasets["genome_file"]})
-
- def add_organism_jbrowse(self):
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
- history_id=self.history,
- tool_inputs={"multiple": "false",
- "name": "foo",
- "unique_id": "bar"})
-
- # Homo sapiens deletion TODO: concat the 2 calls
- def get_sapiens_id(self):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.2",
- history_id=self.history,
- tool_inputs={"genus": "Homo", "species": "species"})
-
- def delete_sapiens(self, hs_id):
- """
- Tool invocation must be as return (or else it executes but returns nothing when called)
- :return:
- """
- return self.instance.tools.run_tool(tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.2",
- history_id=self.history,
- tool_inputs={"organism": str(hs_id)})
-
- def show_pannel(self):
- print(self.instance.tools.get_tool_panel())
- return self.instance.tools.get_tool_panel()