diff --git a/examples/input_demo.yaml b/examples/input_demo.yaml
index 9948a4b02e2028c844774d16b53a9d451788aeb0..79aaaa467ed75781049149e13819a8132d05e7b1 100644
--- a/examples/input_demo.yaml
+++ b/examples/input_demo.yaml
@@ -38,23 +38,4 @@ ectocarpus_sp2_male: # Dummy value the user gives to designate the species (isn
genome_version: "1.0"
# Same as genome version, but for the analysis
ogs_version: ""
- performed_by: ""
-
-# Second example without the comments doc
-ectocarpus_sp2_female:
- description:
- genus: "ectocarpus"
- species: "sp4"
- sex: "female"
- strain: ""
- common_name: ""
- origin: ""
- data:
- parent_directory: "/path/to/closest/parent/dir"
- genome_path: "/path/to/fasta"
- transcripts_path: "/path/to/fasta"
- proteins_path: "/path/to/fasta"
- gff_path: "/path/to/gff"
- genome_version: "1.0"
- ogs_version: "1.0"
- performed_by: ""
+ performed_by: ""
\ No newline at end of file
diff --git a/examples/example.yml b/examples/input_example.yml
similarity index 100%
rename from examples/example.yml
rename to examples/input_example.yml
diff --git a/gga_init.py b/gga_init.py
index 393e5ccd4f487d772f360bf3290b7459a96bce25..b77251c406ec4e091f1e98fe63501dc4dcab2cd7 100644
--- a/gga_init.py
+++ b/gga_init.py
@@ -54,7 +54,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
sys.exit()
# Copy the custom banner to the species dir (banner used in tripal pages)
- if not self.config["custom_banner"] or self.config["custom_banner"] == "/path/to/banner" or self.config["custom_banner"] == "":
+ if not self.config["custom_banner"] or not self.config["custom_banner"] == "/path/to/banner" or not self.config["custom_banner"] == "":
try:
if os.path.isfile(os.path.abspath(self.config["custom_banner"])):
shutil.copy(os.path.abspath(self.config["custom_banner"]), "%s/banner.png" % self.species_dir)
diff --git a/gga_load_data.py b/gga_load_data.py
index ea604318827eca75e3515be37f5a2c74c7c1db83..945d85d3df23c391d0879b00ce56b51b89d7120e 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -124,6 +124,8 @@ class LoadData(speciesData.SpeciesData):
Find source data files in the parent_directory
Link data files
+ TODO: implement search/tests for individual file paths
+
:return:
"""
@@ -483,7 +485,7 @@ class LoadData(speciesData.SpeciesData):
# Need to do it AFTER the datasets import is finished, otherwise the new names are not kept by galaxy
# (erased by metadata generation I guess)
- # ALB: Doesn't work for some reason (LibraryDataset not subscriptable, __getitem__() not implemented)
+ # Doesn't work for some reason (LibraryDataset not subscriptable, __getitem__() not implemented)
# post_renaming[datasets[0]] = clean_name
time.sleep(1)
@@ -508,7 +510,7 @@ class LoadData(speciesData.SpeciesData):
time.sleep(10)
- # ALB: Batch renaming --> Throws a critical error at the moment
+ # Batch renaming --> Throws a critical error at the moment
# logging.info("Import finished, now renaming datasets with pretty names")
# for dataset in post_renaming:
# dataset.update(name=post_renaming[dataset])
@@ -703,7 +705,7 @@ if __name__ == "__main__":
load_data_for_current_species.setup_library()
logging.info("Successfully set up library in galaxy for %s" % load_data_for_current_species.full_name)
- # # Set or get the history for the current organism
+ # Set or get the history for the current organism
load_data_for_current_species.set_get_history()
# Remove H. sapiens from database if here TODO: set a dedicated history for removing H. sapiens (instead of doing it into a species history)
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 5485c6cd207015faa8544cbef30bee1bfd731df9..984c00ffded5ce11cf032f10f01b8a481da14cea 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -8,6 +8,7 @@ import os
import logging
import sys
import json
+import time
import utilities
import speciesData
@@ -218,16 +219,11 @@ class RunWorkflow(speciesData.SpeciesData):
logging.info("Finished initializing instance")
- def run_workflow(self, workflow_path, workflow_parameters, datamap):
+ def run_workflow(self, workflow_path, workflow_parameters, workflow_name, datamap):
"""
- Run the "main" workflow in the galaxy instance
- - import data to library
- - load fasta and gff
- - sync with tripal
- - add jbrowse + organism
- - fill in the tripal views
-
- TODO: map tool name to step id
+ Run a workflow in galaxy
+ Requires the .ga file to be loaded as a dictionary (optionally could be uploaded as a raw file)
+
:param workflow_name:
:param workflow_parameters:
:param datamap:
@@ -235,45 +231,21 @@ class RunWorkflow(speciesData.SpeciesData):
"""
logging.info("Importing workflow: " + str(workflow_path))
- workflow_name = "demo" # for workflow demo
workflow_ga_file = workflow_path
- # Name the workflow in galaxy
- if self.strain != "":
- custom_ga_file = "_".join([self.genus, self.species, self.strain]) + "_workflow.ga"
- custom_ga_file_path = os.path.abspath(custom_ga_file)
- elif self.sex != "":
- custom_ga_file = "_".join([self.genus, self.species, self.sex]) + "_workflow.ga"
- custom_ga_file_path = os.path.abspath(custom_ga_file)
- else:
- custom_ga_file = "_".join([self.genus, self.species]) + "_workflow.ga"
- custom_ga_file_path = os.path.abspath(custom_ga_file)
-
- # Solving format issues in the .ga (encoding errors when importing the file via bioblend)
with open(workflow_ga_file, 'r') as ga_in_file:
- # workflow = str(ga_in_file.readlines())
- # # Ugly fix for the jbrowse parameters (formatting) --> TODO: OBSOLETE (everything set at runtime)
- # workflow = workflow.replace('{\\\\\\\\\\\\"unique_id\\\\\\\\\\\\": \\\\\\\\\\\\"UNIQUE_ID\\\\\\\\\\\\"}',
- # str('{\\\\\\\\\\\\"unique_id\\\\\\\\\\\\": \\\\\\\\\\\\"' + self.genus + " " + self.species) + '\\\\\\\\\\\\"')
- # workflow = workflow.replace('\\\\\\\\\\\\"name\\\\\\\\\\\\": \\\\\\\\\\\\"NAME\\\\\\\\\\\\"',
- # str('\\\\\\\\\\\\"name\\\\\\\\\\\\": \\\\\\\\\\\\"' + self.genus.lower()[0] + self.species) + '\\\\\\\\\\\\"')
- # workflow = workflow.replace("\\\\", "\\") # to restore the correct amount of backslashes in the workflow string before import
-
- # # OBSOLETE
- # workflow = workflow.replace('http://localhost/sp/genus_species/feature/Genus/species/mRNA/{id}',
- # "http://" + self.config["custom_host"] + ":8888/sp/" + self.genus_lowercase+ "_" + self.species + "/feature/" + self.genus + "/mRNA/{id}")
-
- # # The json dict might sometimes turn to be invalid for unknown reasons and the json module will fail to decode it (galaxy export error)
- # workflow = workflow[2:-2] # if the line under doesn't output a correct json
- # # workflow = workflow[:-2] # if the line above doesn't output a correct json
-
# Store the decoded json dictionary
workflow_dict = json.load(ga_in_file)
self.instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
workflow_attributes = self.instance.workflows.get_workflows(name=workflow_name)
workflow_id = workflow_attributes[0]["id"]
+ logging.debug("Workflow ID: %s" % workflow_id)
show_workflow = self.instance.workflows.show_workflow(workflow_id=workflow_id)
+ try:
+ logging.info("Workflow ID: %s" % workflow_id)
+ except Exception:
+ logging.warning("Error retrieving workflow attributes")
logging.debug("Workflow ID: " + workflow_id)
logging.info("Running workflow: %s" % workflow_name)
@@ -368,6 +340,16 @@ class RunWorkflow(speciesData.SpeciesData):
"genus": self.genus_uppercase,
"species": self.chado_species_name,
"common": self.common})
+ time.sleep(3)
+ # Run tool again (sometimes the tool doesn't return anything despite the organism already being in the db)
+ org = self.instance.tools.run_tool(
+ tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.3",
+ history_id=self.history_id,
+ tool_inputs={"abbr": self.abbreviation,
+ "genus": self.genus_uppercase,
+ "species": self.chado_species_name,
+ "common": self.common})
+ time.sleep(10)
org_job_out = org["outputs"][0]["id"]
org_json_output = self.instance.datasets.download_dataset(dataset_id=org_job_out)
try:
@@ -478,7 +460,6 @@ if __name__ == "__main__":
# Set the instance url attribute
for env_variable, value in run_workflow_for_current_organism.config.items():
if env_variable == "custom_host":
- # TODO:
run_workflow_for_current_organism.instance_url = "http://{0}:8888/sp/{1}_{2}/galaxy/".format(
value, run_workflow_for_current_organism.genus_lowercase, run_workflow_for_current_organism.species)
break
@@ -491,95 +472,60 @@ if __name__ == "__main__":
run_workflow_for_current_organism.set_get_history()
# run_workflow_for_current_organism.get_species_history_id()
- # Prepare the instance+history for the current organism (add organism and analyses in Chado) --> add argument?
- # (althought there is no risk as chado refuses to duplicate an analysis/organism)
- # run_workflow_for_current_organism.prepare_history()
+ # Prepare the instance+history for the current organism (add organism and analyses in Chado) TODO: add argument "setup"
+ # (althought it should pose no problem as the "Chado add" refuses to duplicate an analysis/organism anyway)
+ run_workflow_for_current_organism.prepare_history()
# Get the attributes of the instance and project data files
run_workflow_for_current_organism.get_instance_attributes()
run_workflow_for_current_organism.get_organism_and_analyses_ids()
- # Import datasets into history (needs to be done in gga_load_data??)
- # run_workflow_for_current_organism.import_datasets_into_history()
+ # Import datasets into history TODO: put this only for the chado load tripal sync workflow?
+ run_workflow_for_current_organism.import_datasets_into_history()
+ # Explicit workflow parameter names
+ # TODO: Create distinct methods to call different pre-set workflows using CL arguments/config options (i.e load-chado, jbrowse, functional-annotation, orthology, ...)
workflow_parameters = dict()
- # Explicit workflow parameter names
- # TODO: Use an external mapping file instead?
-
- # DEMO WORKFLOW
- PARAM_LOAD_FASTA_IN_HISTORY = "0"
- PARAM_LOAD_FASTA_IN_CHADO = "1"
-
- # Workflow inputs
- workflow_parameters[PARAM_LOAD_FASTA_IN_HISTORY] = {}
- workflow_parameters[PARAM_LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
- "analysis_id": run_workflow_for_current_organism.genome_analysis_id,
- "do_update": "true"}
- # Change "do_update": "true" to "do_update": "false" to prevent appending to the fasta file in chado
- # It is safer to never update it and completely delete and restart the galaxy+tripal services instead (no workaround at the moment)
- run_workflow_for_current_organism.datamap = dict()
+ GENOME_FASTA_FILE = "0"
+ GFF_FILE = "1"
+ PROTEINS_FASTA_FILE = "2"
+ TRANSCRIPTS_FASTA_FILE = "3"
+
+
+ LOAD_FASTA_IN_CHADO = "4"
+ LOAD_GFF_IN_CHADO = "5"
+ SYNC_ORGANISM_INTO_TRIPAL = "6"
+ SYNC_GENOME_ANALYSIS_INTO_TRIPAL = "7"
+ SYNC_OGS_ANALYSIS_INTO_TRIPAL = "8"
+ SYNC_FEATURES_INTO_TRIPAL = "9"
+
+ workflow_parameters[GENOME_FASTA_FILE] = {}
+ workflow_parameters[GFF_FILE] = {}
+ workflow_parameters[PROTEINS_FASTA_FILE] = {}
+ workflow_parameters[TRANSCRIPTS_FASTA_FILE] = {}
+ workflow_parameters[LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
+ "analysis_id": run_workflow_for_current_organism.genome_analysis_id,
+ "do_update": "true"}
+ # Change "do_update": "true" to "do_update": "false" in above parameters to prevent appending to the fasta file in chado
+ # WARNING: It is safer to never update it and just change the genome/ogs versions in the config
+ workflow_parameters[LOAD_GFF_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
+ "analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
+ workflow_parameters[SYNC_ORGANISM_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
+ workflow_parameters[SYNC_GENOME_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
+ workflow_parameters[SYNC_OGS_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.genome_analysis_id}
+ workflow_parameters[SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
# Datamap for input datasets - dataset source (type): ldda (LibraryDatasetDatasetAssociation)
- run_workflow_for_current_organism.datamap[PARAM_LOAD_FASTA_IN_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
-
-
- """COMMENTED FOR THE DEMO"""
- # # Base worflow (loading data in chado and first sync into tripal)
- # PARAM_LOAD_FILE1_INTO_HISTORY, PARAM_LOAD_FILE2_INTO_HISTORY, PARAM_LOAD_FILE3_INTO_HISTORY, PARAM_LOAD_FILE4_INTO_HISTORY = "0", "1", "2", "3"
- # PARAM_LOAD_FASTA_IN_CHADO = "4"
- # PARAM_LOAD_GFF_IN_CHADO = "5"
- # PARAM_SYNC_ORGANISM_INTO_TRIPAL = "6"
- # PARAM_SYNC_GENOME_ANALYSIS_INTO_TRIPAL = "7"
- # PARAM_SYNC_OGS_ANALYSIS_INTO_TRIPAL = "8"
- # PARAM_SYNC_FEATURES_INTO_TRIPAL = "9"
-
-
- # workflow_parameters[PARAM_LOAD_FILE1_INTO_HISTORY] = {}
- # workflow_parameters[PARAM_LOAD_FILE2_INTO_HISTORY] = {}
- # workflow_parameters[PARAM_LOAD_FILE3_INTO_HISTORY] = {}
- # workflow_parameters[PARAM_LOAD_FILE4_INTO_HISTORY] = {}
- # workflow_parameters[PARAM_LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
- # "analysis_id": run_workflow_for_current_organism.genome_analysis_id,
- # "do_update": "true"}
- # workflow_parameters[PARAM_LOAD_GFF_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
- # "analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
- # workflow_parameters[PARAM_SYNC_ORGANISM_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
- # workflow_parameters[PARAM_SYNC_GENOME_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
- # workflow_parameters[PARAM_SYNC_OGS_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.genome_analysis_id}
- # workflow_parameters[PARAM_SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
-
- # Loading files into history works a bit different than the others as it's not a GMOD tool but a standard Galaxy tool
- # It requires this additional "datamap" (conveniently named "datamap" here), requiring the source type of the file and its corresponding ID (unique)
- # The comments taken from the bioblend docs:
- # """
- # A mapping of workflow inputs to datasets and dataset collections.
- # The datasets source can be a LibraryDatasetDatasetAssociation (``ldda``),
- # LibraryDataset (``ld``), HistoryDatasetAssociation (``hda``), or
- # HistoryDatasetCollectionAssociation (``hdca``).
- #
- # The map must be in the following format:
- # ``{'<input_index>': {'id': <encoded dataset ID>, 'src': '[ldda, ld, hda, hdca]'}}``
- # (e.g. ``{'2': {'id': '29beef4fadeed09f', 'src': 'hda'}}``)
- #
- # This map may also be indexed by the UUIDs of the workflow steps,
- # as indicated by the ``uuid`` property of steps returned from the
- # Galaxy API. Alternatively workflow steps may be addressed by
- # the label that can be set in the workflow editor. If using
- # uuid or label you need to also set the ``inputs_by`` parameter
- # to ``step_uuid`` or ``name``.
- # """
- # run_workflow_for_current_organism.datamap = dict()
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE1_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE2_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE3_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
- # run_workflow_for_current_organism.datamap[PARAM_LOAD_FILE4_INTO_HISTORY] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
-
- # Run the workflow with the parameters set above
+ run_workflow_for_current_organism.datamap = dict()
+ run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
+ run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
+ run_workflow_for_current_organism.datamap[PROTEINS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
+ run_workflow_for_current_organism.datamap[TRANSCRIPTS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
+
+ # Run the Chado load Tripal sync workflow with the parameters set above
run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
workflow_parameters=workflow_parameters,
- datamap=run_workflow_for_current_organism.datamap)
-
- # WIP: metadata
- # metadata[genus_species_strain_sex]["workflows_run"] = metadata[genus_species_strain_sex]["workflows_run"].append("fooS")
+ datamap=run_workflow_for_current_organism.datamap,
+ workflow_name="Chado load Tripal synchronize")
diff --git a/templates/nginx_apollo_template.conf b/templates/nginx_apollo.conf
similarity index 100%
rename from templates/nginx_apollo_template.conf
rename to templates/nginx_apollo.conf
diff --git a/templates/nginx_download_template.conf b/templates/nginx_download.conf
similarity index 100%
rename from templates/nginx_download_template.conf
rename to templates/nginx_download.conf
diff --git a/workflows/Chado_load_Tripal_synchronize.ga b/workflows/Chado_load_Tripal_synchronize.ga
new file mode 100644
index 0000000000000000000000000000000000000000..a194b03268c48c4300a3b2a0f6b759cbf0fb6c6b
--- /dev/null
+++ b/workflows/Chado_load_Tripal_synchronize.ga
@@ -0,0 +1,413 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "Chado load Tripal synchronize",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 200
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "89e7487e-004d-4db1-b5eb-1676b98aebde",
+ "workflow_outputs": []
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 290
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "1d25f54c-7575-4c8d-be55-73dd7e58613f",
+ "workflow_outputs": []
+ },
+ "2": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 2,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 380
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "6c1a20fa-828a-404c-b107-76fb8ddf3954",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 3,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 470
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "74f22d9b-e764-45e4-b0eb-579c9b647ea0",
+ "workflow_outputs": []
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "fasta": {
+ "id": 3,
+ "output_name": "output"
+ },
+ "wait_for": {
+ "id": 3,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "fasta"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "wait_for"
+ }
+ ],
+ "label": null,
+ "name": "Chado load fasta",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "json"
+ }
+ ],
+ "position": {
+ "left": 486,
+ "top": 200
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "ba4d07fbaf47",
+ "name": "chado_feature_load_fasta",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"analysis_id\": \"1\", \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism\": \"2\", \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.4+galaxy0",
+ "type": "tool",
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similarity index 100%
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