diff --git a/.gitignore b/.gitignore
index f83e8cf..eacd853 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,7 @@
.idea
target
*.iml
+/.classpath
+/.project
+/.settings
+/bin
diff --git a/pom.xml b/pom.xml
index 316900d..9380298 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,75 +1,89 @@
- 4.0.0
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ 4.0.0
- ca.tom
- testPlugin
- 1.0-SNAPSHOT
+ ca.tom
+ example-plugin
+ 1.0-SNAPSHOT
-
-
- ca.corefacility.bioinformatics
- irida
- 0.23.0-SNAPSHOT
- classes
-
+
+
+ example-plugin
+ ca.corefacility.bioinformatics.irida.plugins.ExamplePlugin
+ 0.1.0
+ Aaron Petkau
+ 1.0.0
-
- org.pf4j
- pf4j
- 2.3.0
- provided
-
-
+
+ 0.23.0-SNAPSHOT
+
+
+ 2.4.0
-
-
-
-
- org.apache.maven.plugins
- maven-compiler-plugin
- 3.1
-
- 1.8
- 1.8
- true
-
-
+
+ 1.8
+
-
- org.apache.maven.plugins
- maven-jar-plugin
+
+
+ ca.corefacility.bioinformatics
+ irida
+ ${irida.version}
+ classes
+
-
-
-
- ca.corefacility.bioinformatics.irida.ExamplePlugin
- plugin-example
- Tom Matthews
- 0.0.1
-
-
-
-
+
+ org.pf4j
+ pf4j
+ ${pf4j.version}
+ provided
+
+
-
- org.apache.maven.plugins
- maven-assembly-plugin
- 2.6
-
-
- jar-with-dependencies
-
-
-
+
+
+
+ org.apache.maven.plugins
+ maven-compiler-plugin
+ 3.1
+
+ ${java.version}
+ ${java.version}
+ true
+
+
-
-
-
-
+
+ org.apache.maven.plugins
+ maven-jar-plugin
+
+
+
+ ${plugin.class}
+ ${plugin.dependencies}
+ ${plugin.id}
+ ${plugin.provider}
+ ${plugin.version}
+ ${plugin.requires}
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-assembly-plugin
+ 2.6
+
+
+ jar-with-dependencies
+
+
+
+
+
diff --git a/src/main/java/ca/corefacility/bioinformatics/irida/ExamplePlugin.java b/src/main/java/ca/corefacility/bioinformatics/irida/ExamplePlugin.java
deleted file mode 100644
index 559f226..0000000
--- a/src/main/java/ca/corefacility/bioinformatics/irida/ExamplePlugin.java
+++ /dev/null
@@ -1,58 +0,0 @@
-package ca.corefacility.bioinformatics.irida;
-
-import ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSampleUpdater;
-import ca.corefacility.bioinformatics.irida.plugins.IridaPlugin;
-import ca.corefacility.bioinformatics.irida.plugins.IridaPluginException;
-import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
-import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
-import org.pf4j.Extension;
-import org.pf4j.Plugin;
-import org.pf4j.PluginException;
-import org.pf4j.PluginWrapper;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Optional;
-import java.util.Properties;
-
-/**
- * An example {@link IridaPlugin} implementation
- */
-public class ExamplePlugin extends Plugin {
-
- public ExamplePlugin(PluginWrapper wrapper) {
- super(wrapper);
- }
-
- @Override
- public void start() throws PluginException {
- System.out.println("Example IRIDA plugin loaded");
- }
-
- @Extension
- public static class PluginInfo implements IridaPlugin {
-
- @Override
- public Properties getMessages() throws IridaPluginException {
-
- ClassLoader classLoader = getClass().getClassLoader();
-
- Properties prop = new Properties();
-
- try (InputStream resourceAsStream = classLoader.getResourceAsStream("messages/messages_en.properties");) {
- prop.load(resourceAsStream);
- } catch (IOException e) {
- throw new IridaPluginException("Cannot load messages", e);
- }
-
- return prop;
- }
-
- @Override
- public Optional getUpdater(MetadataTemplateService metadataTemplateService,
- SampleService sampleService) {
- return Optional.empty();
- }
- }
-
-}
diff --git a/src/main/java/ca/corefacility/bioinformatics/irida/plugins/ExamplePlugin.java b/src/main/java/ca/corefacility/bioinformatics/irida/plugins/ExamplePlugin.java
new file mode 100644
index 0000000..c418c14
--- /dev/null
+++ b/src/main/java/ca/corefacility/bioinformatics/irida/plugins/ExamplePlugin.java
@@ -0,0 +1,76 @@
+package ca.corefacility.bioinformatics.irida.plugins;
+
+import java.awt.Color;
+import java.util.Optional;
+import java.util.UUID;
+
+import org.pf4j.Extension;
+import org.pf4j.Plugin;
+import org.pf4j.PluginWrapper;
+
+import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType;
+import ca.corefacility.bioinformatics.irida.plugins.IridaPlugin;
+
+/**
+ * An example {@link IridaPlugin} implementation
+ */
+public class ExamplePlugin extends Plugin {
+
+ public ExamplePlugin(PluginWrapper wrapper) {
+ super(wrapper);
+ }
+
+ @Extension
+ public static class PluginInfo implements IridaPlugin {
+
+ /***************************************************************************************
+ * Required methods
+ *
+ * These methods are required to be overridden when implementing a pipeline as a plugin.
+ ***************************************************************************************/
+
+ /**
+ * Gets the particular {@link AnalysisType} object for this workflow.
+ * This should correspond to the analysisType entry in the irida_workflow.xml file.
+ *
+ * {@code FIRST_LINES }
+ */
+ @Override
+ public AnalysisType getAnalysisType() {
+ return new AnalysisType("FIRST_LINES");
+ }
+
+ /**
+ * Gets the particular workflow id.
+ * This should correspond to the id entry in the irida_workflow.xml file.
+ *
+ * {@code c07a0d4c-fb53-4183-8ded-298f8a4decca }
+ */
+ @Override
+ public UUID getDefaultWorkflowUUID() {
+ return UUID.fromString("c07a0d4c-fb53-4183-8ded-298f8a4decca");
+ }
+
+ /*********************************************************************************************************************
+ * Optional methods.
+ *
+ * These methods are not required to be overridden but can be used to adjust the appearance/behaviour of the pipeline.
+ *********************************************************************************************************************/
+
+ /**
+ * Defines the background color in the IRIDA UI corresponding to this pipeline.
+ */
+ @Override
+ public Optional getBackgroundColor() {
+ return Optional.of(Color.decode("#7fcdbb"));
+ }
+
+ /**
+ * Defines the text color in the IRIDA UI corresponding to this pipeline.
+ */
+ @Override
+ public Optional getTextColor() {
+ return Optional.of(Color.BLACK);
+ }
+ }
+}
diff --git a/src/main/resources/messages/messages_en.properties b/src/main/resources/messages/messages_en.properties
deleted file mode 100644
index 0e0d774..0000000
--- a/src/main/resources/messages/messages_en.properties
+++ /dev/null
@@ -1 +0,0 @@
-irida.plugin.message=Example message from plugin
\ No newline at end of file
diff --git a/src/main/resources/workflows/0.1.0/irida_workflow.xml b/src/main/resources/workflows/0.1.0/irida_workflow.xml
new file mode 100644
index 0000000..106a859
--- /dev/null
+++ b/src/main/resources/workflows/0.1.0/irida_workflow.xml
@@ -0,0 +1,20 @@
+
+
+ c07a0d4c-fb53-4183-8ded-298f8a4decca
+ FirstLines
+ 0.1.0
+ FIRST_LINES
+
+ fastq_paired
+ true
+
+
+
+
+
+
+
+
diff --git a/src/main/resources/workflows/0.1.0/irida_workflow_structure.ga b/src/main/resources/workflows/0.1.0/irida_workflow_structure.ga
new file mode 100644
index 0000000..625fc38
--- /dev/null
+++ b/src/main/resources/workflows/0.1.0/irida_workflow_structure.ga
@@ -0,0 +1,192 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "Select first number of lines",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "fastq_paired"
+ }
+ ],
+ "label": "fastq_paired",
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 200
+ },
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"fastq_paired\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "uuid": "6c0e8d85-c804-45e9-b353-6cd5594e7299",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "dd7723a2-b3d0-49de-9ad1-c6c625456ed6"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": "Show beginning1",
+ "errors": null,
+ "id": 1,
+ "input_connections": {
+ "input": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Select first",
+ "name": "input"
+ }
+ ],
+ "label": null,
+ "name": "Select first",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 464,
+ "top": 200
+ },
+ "post_job_actions": {
+ "HideDatasetActionout_file1": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "out_file1"
+ }
+ },
+ "tool_id": "Show beginning1",
+ "tool_state": "{\"__page__\": 0, \"lineNum\": \"\\\"4\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "uuid": "081b906f-0325-4189-8e55-c507211f59e9",
+ "workflow_outputs": []
+ },
+ "2": {
+ "annotation": "",
+ "content_id": "__UNZIP_COLLECTION__",
+ "errors": null,
+ "id": 2,
+ "input_connections": {
+ "input": {
+ "id": 1,
+ "output_name": "out_file1"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Unzip Collection",
+ "name": "input"
+ }
+ ],
+ "label": null,
+ "name": "Unzip Collection",
+ "outputs": [
+ {
+ "name": "forward",
+ "type": "data"
+ },
+ {
+ "name": "reverse",
+ "type": "data"
+ }
+ ],
+ "position": {
+ "left": 692,
+ "top": 200
+ },
+ "post_job_actions": {
+ "HideDatasetActionforward": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "forward"
+ },
+ "HideDatasetActionreverse": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
+ "output_name": "reverse"
+ }
+ },
+ "tool_id": "__UNZIP_COLLECTION__",
+ "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "uuid": "70dcb263-50f5-4de1-9a2b-e08c5e5660fc",
+ "workflow_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "cat1",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "input1": {
+ "id": 2,
+ "output_name": "forward"
+ },
+ "queries_0|input2": {
+ "id": 2,
+ "output_name": "reverse"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Concatenate datasets",
+ "name": "input1"
+ }
+ ],
+ "label": null,
+ "name": "Concatenate datasets",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 921,
+ "top": 200
+ },
+ "post_job_actions": {
+ "RenameDatasetActionout_file1": {
+ "action_arguments": {
+ "newname": "first-lines.txt"
+ },
+ "action_type": "RenameDatasetAction",
+ "output_name": "out_file1"
+ }
+ },
+ "tool_id": "cat1",
+ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"queries\": \"[{\\\"input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__index__\\\": 0}]\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "uuid": "5daee5ef-60f5-4e91-9903-a0a2883ccdba",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "out_file1",
+ "uuid": "06d34b1b-eca6-4c40-b42b-e3983156a5ff"
+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "ebebd999-93a2-4fe8-aa22-c45303703f1b"
+}
diff --git a/src/main/resources/workflows/0.1.0/messages_en.properties b/src/main/resources/workflows/0.1.0/messages_en.properties
new file mode 100644
index 0000000..ea54488
--- /dev/null
+++ b/src/main/resources/workflows/0.1.0/messages_en.properties
@@ -0,0 +1,10 @@
+#Pipeline Info Properties
+#Thu Aug 30 14:51:58 CDT 2018
+pipeline.h1.FirstLines=FirstLines Pipeline
+pipeline.title.FirstLines=Pipelines - FirstLines
+workflow.FIRST_LINES.title=FirstLines Pipeline
+workflow.FIRST_LINES.description=
+pipeline.parameters.modal-title.firstlines=FirstLines Pipeline Parameters
+#Tool Parameters - Tool: Show beginning1 - Workflow Step #: 1
+#Thu Aug 30 14:51:58 CDT 2018
+pipeline.parameters.firstlines.show-beginning1-1-lineNum=Number of lines from each file