Merge branch 'development'

phac-nml · Mar 5, 2021 · cd424e0 · cd424e0
2 parents c4f18c0 + 4e83146
commit cd424e0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,7 +2,7 @@
 
 * Updated writing of metadata to be compatible with IRIDA `21.01` update.
    * This means the plugin now requires IRIDA `21.01+`.
-* Updated staramr version to `0.7.1`.
+* Updated staramr version to `0.7.2`.
    * The plugin will now save the additional fields provided by the newer staramr version in the metadata table.
 * Updated RGI version to `5.1.1`.
 * Updated Shovill to version `1.1.0`.

diff --git a/README.md b/README.md
@@ -36,7 +36,7 @@ In order to use this pipeline, you will also have to install the [RGI][], [stara
 | Name    | Version          | Galaxy Tool                                                    |
 |---------|------------------|----------------------------------------------------------------|
 | RGI     | `5.1.1`          | <https://toolshed.g2.bx.psu.edu/view/card/rgi/bfbfc24c5af2>    |
-| staramr | `0.7.1+galaxy2`  | <https://toolshed.g2.bx.psu.edu/view/nml/staramr/2fd4d4c9c5c2> |
+| staramr | `0.7.2+galaxy0`  | <https://toolshed.g2.bx.psu.edu/view/nml/staramr/4b9a8031ab74> |
 | shovill | `1.1.0+galaxy0`  | <https://toolshed.g2.bx.psu.edu/view/iuc/shovill/83ead2be47b2> |
 
 # Tutorial

diff --git a/src/main/resources/workflows/0.2.0/irida_workflow.xml b/src/main/resources/workflows/0.2.0/irida_workflow.xml
@@ -40,52 +40,52 @@
       <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="assembler"/>
     </parameter>
     <parameter name="staramr-2-use_pointfinder" defaultValue="disabled">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="use_pointfinder"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="use_pointfinder"/>
     </parameter>
     <parameter name="staramr-2-advanced.plength_plasmidfinder" defaultValue="60.0">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.plength_plasmidfinder"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.plength_plasmidfinder"/>
     </parameter>
     <parameter name="staramr-2-advanced.exclude_negatives" defaultValue="false">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.exclude_negatives"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.exclude_negatives"/>
     </parameter>
     <parameter name="staramr-2-advanced.plength_resfinder" defaultValue="60.0">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.plength_resfinder"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.plength_resfinder"/>
     </parameter>
     <parameter name="staramr-2-advanced.genome_size_lower_bound" defaultValue="4000000">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.genome_size_lower_bound"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.genome_size_lower_bound"/>
     </parameter>
     <parameter name="staramr-2-advanced.mlst_scheme" defaultValue="auto">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.mlst_scheme"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.mlst_scheme"/>
     </parameter>
     <parameter name="staramr-2-advanced.exclude_genes.exclude_genes_condition" defaultValue="default">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.exclude_genes.exclude_genes_condition"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.exclude_genes.exclude_genes_condition"/>
     </parameter>
     <parameter name="staramr-2-advanced.plength_pointfinder" defaultValue="95.0">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.plength_pointfinder"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.plength_pointfinder"/>
     </parameter>
     <parameter name="staramr-2-advanced.minimum_contig_length" defaultValue="300">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.minimum_contig_length"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.minimum_contig_length"/>
     </parameter>
     <parameter name="staramr-2-advanced.minimum_N50_value" defaultValue="10000">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.minimum_N50_value"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.minimum_N50_value"/>
     </parameter>
     <parameter name="staramr-2-advanced.genome_size_upper_bound" defaultValue="6000000">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.genome_size_upper_bound"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.genome_size_upper_bound"/>
     </parameter>
     <parameter name="staramr-2-advanced.exclude_resistance_phenotypes" defaultValue="false">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.exclude_resistance_phenotypes"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.exclude_resistance_phenotypes"/>
     </parameter>
     <parameter name="staramr-2-advanced.plasmidfinder_type" defaultValue="include_all">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.plasmidfinder_type"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.plasmidfinder_type"/>
     </parameter>
     <parameter name="staramr-2-advanced.report_all_blast" defaultValue="false">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.report_all_blast"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.report_all_blast"/>
     </parameter>
     <parameter name="staramr-2-advanced.unacceptable_number_contigs" defaultValue="1000">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.unacceptable_number_contigs"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.unacceptable_number_contigs"/>
     </parameter>
     <parameter name="staramr-2-advanced.pid_threshold" defaultValue="98.0">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2" parameterName="advanced.pid_threshold"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.2+galaxy0" parameterName="advanced.pid_threshold"/>
     </parameter>
     <parameter name="rgi-3-low_quality" defaultValue="false">
       <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.1.1" parameterName="low_quality"/>
@@ -131,7 +131,7 @@
       <name>staramr</name>
       <owner>nml</owner>
       <url>https://toolshed.g2.bx.psu.edu</url>
-      <revision>2fd4d4c9c5c2</revision>
+      <revision>4b9a8031ab74</revision>
     </repository>
   </toolRepositories>
 </iridaWorkflow>