diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index a8d3476c1c6..5d69c9418a7 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -214,7 +214,14 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase, ImporterGalaxyInterface ):
input_type = value["type"]
if input_type == "File":
content = read_test_data(value)
- hda = self.dataset_populator.new_dataset( history_id, content=content )
+ new_dataset_kwds = {
+ "content": content
+ }
+ if "name" in value:
+ new_dataset_kwds["name"] = value["name"]
+ if "file_type" in value:
+ new_dataset_kwds["file_type"] = value["file_type"]
+ hda = self.dataset_populator.new_dataset( history_id, **new_dataset_kwds )
label_map[key] = self._ds_entry( hda )
has_uploads = True
elif input_type == "raw":
@@ -1251,6 +1258,104 @@ test_data:
content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
assert content[ "name" ] == "foo was replaced"
+ @skip_without_tool( "cat" )
+ def test_run_rename_based_on_input( self ):
+ history_id = self.dataset_populator.new_history()
+ self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+ - id: input1
+steps:
+ - tool_id: cat
+ label: first_cat
+ state:
+ input1:
+ $link: input1
+ outputs:
+ out_file1:
+ rename: "#{input1 | basename} suffix"
+test_data:
+ input1:
+ value: 1.fasta
+ type: File
+ name: fasta1
+""", history_id=history_id)
+ content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
+ name = content[ "name" ]
+ assert name == "fasta1 suffix", name
+
+ @skip_without_tool( "cat" )
+ def test_run_rename_based_on_input_repeat( self ):
+ history_id = self.dataset_populator.new_history()
+ self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+ - id: input1
+ - id: input2
+steps:
+ - tool_id: cat
+ label: first_cat
+ state:
+ input1:
+ $link: input1
+ queries:
+ - input2:
+ $link: input2
+ outputs:
+ out_file1:
+ rename: "#{queries_0.input2| basename} suffix"
+test_data:
+ input1:
+ value: 1.fasta
+ type: File
+ name: fasta1
+ input2:
+ value: 1.fasta
+ type: File
+ name: fasta2
+""", history_id=history_id)
+ content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
+ name = content[ "name" ]
+ assert name == "fasta2 suffix", name
+
+ @skip_without_tool( "mapper2" )
+ def test_run_rename_based_on_input_conditional( self ):
+ history_id = self.dataset_populator.new_history()
+ self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+ - id: fasta_input
+ - id: fastq_input
+steps:
+ - tool_id: mapper2
+ state:
+ fastq_input:
+ fastq_input_selector: single
+ fastq_input1:
+ $link: fastq_input
+ reference:
+ $link: fasta_input
+ outputs:
+ out_file1:
+ # Wish it was qualified for conditionals but it doesn't seem to be. -John
+ # rename: "#{fastq_input.fastq_input1 | basename} suffix"
+ rename: "#{fastq_input1 | basename} suffix"
+test_data:
+ fasta_input:
+ value: 1.fasta
+ type: File
+ name: fasta1
+ file_type: fasta
+ fastq_input:
+ value: 1.fastqsanger
+ type: File
+ name: fastq1
+ file_type: fastqsanger
+""", history_id=history_id)
+ content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
+ name = content[ "name" ]
+ assert name == "fastq1 suffix", name
+
@skip_without_tool( "cat1" )
def test_run_with_runtime_pja( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_pja_runtime" )
diff --git a/test/functional/tools/for_workflows/mapper2.xml b/test/functional/tools/for_workflows/mapper2.xml
new file mode 100644
index 00000000000..3b355c6628c
--- /dev/null
+++ b/test/functional/tools/for_workflows/mapper2.xml
@@ -0,0 +1,33 @@
+
+
+ cp $__tool_directory__/1.bam $out_file1
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diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index ccef907c6a1..58ecb3b6f5a 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -114,6 +114,7 @@
+