Prepare for v0.2

Public-Health-Bioinformatics · Jan 2, 2020 · 4860cfd · 4860cfd
1 parent 9d3ab1b
commit 4860cfd
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Showing 5 changed files with 489 additions and 4 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,14 +6,14 @@
 
 	<groupId>org.publichealthbioinformatics</groupId>
 	<artifactId>irida-plugin-resistance-screen</artifactId>
-	<version>0.1.1</version>
+	<version>0.2.0-SNAPSHOT</version>
 
 	<!-- Please fill out these properties with information about your particular plugin -->
 	<properties>
 		<!-- Information used to define properties about a plugin. Please see the PF4J docs for more details https://pf4j.org/doc/getting-started.html -->
 		<plugin.id>resistance-screen</plugin.id>
 		<plugin.class>org.publichealthbioinformatics.irida.plugin.resistancescreen.ResistanceScreenPlugin</plugin.class>
-		<plugin.version>0.1.1</plugin.version>
+		<plugin.version>0.2.0-SNAPSHOT</plugin.version>
 		<plugin.provider>Dan Fornika</plugin.provider>
 		<plugin.dependencies></plugin.dependencies>
 		<plugin.requires.runtime>1.0.0</plugin.requires.runtime>

diff --git a/.../org/publichealthbioinformatics/irida/plugin/resistancescreen/ResistanceScreenPlugin.java b/.../org/publichealthbioinformatics/irida/plugin/resistancescreen/ResistanceScreenPlugin.java
@@ -70,14 +70,14 @@ public AnalysisType getAnalysisType() {
 		 * <strong>id</strong> entry in the <strong>irida_workflow.xml</strong> file.
 		 * 
 		 * <pre>
-		 * {@code <id>ca1a52d1-871e-41ff-8a72-ac828f27da86</id>}
+		 * {@code <id>1f40bbf2-4080-4cf7-a846-988e602eaa30</id>}
 		 * </pre>
 		 * 
 		 * @return A {@link UUID} defining the id of this pipeline.
 		 */
 		@Override
 		public UUID getDefaultWorkflowUUID() {
-			return UUID.fromString("ca1a52d1-871e-41ff-8a72-ac828f27da86");
+			return UUID.fromString("1f40bbf2-4080-4cf7-a846-988e602eaa30");
 		}
 
 		/*******************************************************************************

diff --git a/src/main/resources/workflows/0.2.0/irida_workflow.xml b/src/main/resources/workflows/0.2.0/irida_workflow.xml
@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<iridaWorkflow>
+  <id>1f40bbf2-4080-4cf7-a846-988e602eaa30</id>
+  <name>resistance-screen</name>
+  <version>0.1.1</version>
+  <analysisType>RESISTANCE_SCREEN</analysisType>
+  <inputs>
+    <sequenceReadsPaired>sequence_reads_paired</sequenceReadsPaired>
+    <requiresSingleSample>true</requiresSingleSample>
+  </inputs>
+  <parameters>
+    <parameter name="shovill-1-adv.nocorr" defaultValue="true">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="adv.nocorr" label="Disable post-assembly correction" type="boolean"/>
+    </parameter>
+    <parameter name="shovill-1-adv.mincov" defaultValue="2">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="adv.mincov" label="Minimum contig coverage" type="integer"/>
+    </parameter>
+    <parameter name="shovill-1-trim" defaultValue="true">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="trim" label="Trim reads" type="boolean"/>
+    </parameter>
+    <parameter name="shovill-1-adv.namefmt" defaultValue="contig%05d">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="adv.namefmt" label="Contig name format" type="text"/>
+    </parameter>
+    <parameter name="shovill-1-adv.depth" defaultValue="100">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="adv.depth" label="Depth" type="integer"/>
+    </parameter>
+    <parameter name="shovill-1-adv.gsize" defaultValue="">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="adv.gsize" label="Estimated genome size" type="text"/>
+    </parameter>
+    <parameter name="shovill-1-adv.opts" defaultValue="">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="adv.opts" label="Extra SPAdes options" type="text"/>
+    </parameter>
+    <parameter name="shovill-1-adv.minlen" defaultValue="0">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="adv.minlen" label="Minimum contig length" type="integer"/>
+    </parameter>
+    <parameter name="shovill-1-assembler" defaultValue="spades">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4" parameterName="assembler" label="Assembler to use" type="select"/>
+    </parameter>
+    <parameter name="abricate-2-adv.db" defaultValue="card">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.9.8" parameterName="adv.db"/>
+    </parameter>
+    <parameter name="abricate-2-adv.min_dna_id" defaultValue="75.0">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.9.8" parameterName="adv.min_dna_id"/>
+    </parameter>
+    <parameter name="screen_abricate_report-3-abricate_screening_file" required="true">
+      <dynamicSource>
+          <galaxyToolDataTable name="abricate_report_screening_files" displayColumn="name" parameterColumn="value" />
+      </dynamicSource>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/public-health-bioinformatics/screen_abricate_report/screen_abricate_report/0.1.0" parameterName="screening_file"/>
+    </parameter>
+  </parameters>
+  <outputs>
+    <output name="abricate_report_screened" fileName="abricate_report_screened.tsv"/>
+    <output name="gene_detection_status" fileName="gene_detection_status.tsv"/>
+    <output name="abricate_report_full" fileName="abricate_report_full.tsv"/>
+    <output name="quast" fileName="quast.tsv"/>
+    <output name="assembly" fileName="assembly.fasta"/>
+  </outputs>
+  <toolRepositories>
+    <repository>
+      <name>shovill</name>
+      <owner>iuc</owner>
+      <url>https://toolshed.g2.bx.psu.edu</url>
+      <revision>865119fcb694</revision>
+    </repository>
+    <repository>
+      <name>quast</name>
+      <owner>iuc</owner>
+      <url>https://toolshed.g2.bx.psu.edu</url>
+      <revision>59db8ea8c845</revision>
+    </repository>
+    <repository>
+      <name>abricate</name>
+      <owner>iuc</owner>
+      <url>https://toolshed.g2.bx.psu.edu</url>
+      <revision>4efdca267d51</revision>
+    </repository>
+    <repository>
+      <name>screen_abricate_report</name>
+      <owner>public-health-bioinformatics</owner>
+      <url>https://toolshed.g2.bx.psu.edu</url>
+      <revision>b2d56a44a872</revision>
+    </repository>
+    <repository>
+      <name>data_manager_manual</name>
+      <owner>iuc</owner>
+      <url>https://toolshed.g2.bx.psu.edu</url>
+      <revision>744f607fac50</revision>
+    </repository>
+  </toolRepositories>
+</iridaWorkflow>