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Add pipeline v0.2.0 with snp-dists SNP distance matrix #6

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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -36,6 +36,7 @@ managers within your Galaxy instance. These can be found at:
| snippy | `4.4.5` | `iuc` | 10 (2020-01-30) | [snippy-10:3fe8ef358d66](https://toolshed.g2.bx.psu.edu/view/iuc/snippy/3fe8ef358d66) |
| gubbins | `2.2.1` | `iuc` | 0 (2017-06-23) | [gubbins-0:637ec5d5368c](https://toolshed.g2.bx.psu.edu/view/iuc/gubbins/637ec5d5368c) |
| snp_sites | `2.5.1` | `iuc` | 1 (2019-11-02) | [snp_sites-1:5804f786060d](https://toolshed.g2.bx.psu.edu/view/iuc/snp_sites/5804f786060d) |
| snp_dists | `0.6.3` | `iuc` | 0 (2019-10-19) | [snp_dists-0:1959cc43b414](https://toolshed.g2.bx.psu.edu/view/iuc/snp_dists/1959cc43b414) |
| iqtree | `1.5.5.3` | `iuc` | 4 (2020-04-03) | [iqtree-4:f97743d52b87](https://toolshed.g2.bx.psu.edu/view/iuc/iqtee/f97743d52b87) |

**NOTE**: There is currently an unresolved issue in snippy involving a problem resolving the correct version number for samtools. This issue arises when snippy is installed from bioconda, as is normally the case when installing to galaxy. The issue can be resolved by:
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4 changes: 2 additions & 2 deletions pom.xml
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Expand Up @@ -6,14 +6,14 @@

<groupId>org.publichealthbioinformatics</groupId>
<artifactId>irida-plugin-snippy-phylogenomics</artifactId>
<version>0.1.1</version>
<version>0.2.0</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>snippy-phylogenomics</plugin.id>
<plugin.class>org.publichealthbioinformatics.irida.plugin.snippyphylogenomics.SnippyPhylogenomicsPlugin</plugin.class>
<plugin.version>0.1.1</plugin.version>
<plugin.version>0.2.0</plugin.version>
<plugin.provider>Dan Fornika</plugin.provider>
<plugin.dependencies></plugin.dependencies>
<plugin.requires.runtime>1.0.0</plugin.requires.runtime>
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4 changes: 2 additions & 2 deletions ...ublichealthbioinformatics/irida/plugin/snippyphylogenomics/SnippyPhylogenomicsPlugin.java
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Expand Up @@ -72,14 +72,14 @@ public AnalysisType getAnalysisType() {
* <strong>id</strong> entry in the <strong>irida_workflow.xml</strong> file.
*
* <pre>
* {@code <id>bd535929-cef1-4d03-9354-61e0d43945d9</id>}
* {@code <id>b27aa2b7-bca9-4271-9023-52d077077404</id>}
* </pre>
*
* @return A {@link UUID} defining the id of this pipeline.
*/
@Override
public UUID getDefaultWorkflowUUID() {
return UUID.fromString("bd535929-cef1-4d03-9354-61e0d43945d9");
return UUID.fromString("b27aa2b7-bca9-4271-9023-52d077077404");
}

/*******************************************************************************
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86 changes: 86 additions & 0 deletions src/main/resources/workflows/0.2.0/irida_workflow.xml
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<?xml version="1.0" encoding="UTF-8"?>
<iridaWorkflow>
<id>b27aa2b7-bca9-4271-9023-52d077077404</id>
<name>snippy-phylogenomics</name>
<version>0.2.0</version>
<analysisType>SNIPPY_PHYLOGENOMICS</analysisType>
<inputs>
<sequenceReadsPaired>sequence_reads_paired</sequenceReadsPaired>
<reference>reference</reference>
<requiresSingleSample>false</requiresSingleSample>
</inputs>
<parameters>
<parameter name="snippy-2-adv.minfrac" defaultValue="0.9">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.4.5+galaxy2" parameterName="adv.minfrac"/>
</parameter>
<parameter name="snippy-2-adv.mincov" defaultValue="10">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.4.5+galaxy2" parameterName="adv.mincov"/>
</parameter>
<parameter name="snippy-2-adv.mapqual" defaultValue="60">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.4.5+galaxy2" parameterName="adv.mapqual"/>
</parameter>
<parameter name="snippy-2-adv.minqual" defaultValue="100.0">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.4.5+galaxy2" parameterName="adv.minqual"/>
</parameter>
<parameter name="gubbins-5-really_adv.max_window_size" defaultValue="10000">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0" parameterName="really_adv.max_window_size" label="Maximum Window Size" type="integer"/>
</parameter>
<parameter name="gubbins-5-really_adv.min_snps" defaultValue="3">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0" parameterName="really_adv.min_snps" label="Minimum SNPS" type="integer"/>
</parameter>
<parameter name="gubbins-5-really_adv.min_window_size" defaultValue="100">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0" parameterName="really_adv.min_window_size" label="Minimum Window Size" type="integer"/>
</parameter>
<parameter name="gubbins-5-really_adv.filter_percentage" defaultValue="25">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0" parameterName="really_adv.filter_percentage" label="Filter Percentage" type="integer"/>
</parameter>
<parameter name="iqtree-7-modelling_parameters.automatic_model.cond_model.m" defaultValue="GTR+G+ASC">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3" parameterName="modelling_parameters.automatic_model.cond_model.m"/>
</parameter>
<parameter name="iqtree-8-general_options.short_alignments" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3" parameterName="general_options.short_alignments"/>
</parameter>
</parameters>
<outputs>
<output name="core_snps_pre_filter" fileName="core_snps_pre_filter.fasta"/>
<output name="core_snps_pre_recomb_filter" fileName="core_snps_pre_recomb_filter.fasta"/>
<output name="predicted_recombinant_sites" fileName="predicted_recombinant_sites.gff"/>
<output name="core_snps_post_recomb_filter" fileName="core_snps_post_recomb_filter.fasta"/>
<output name="tree_report" fileName="tree_report.txt"/>
<output name="tree" fileName="max_likelihood_tree.newick"/>
<output name="max_likelihood_distance_matrix" fileName="max_likelihood_distance_matrix.txt"/>
<output name="snp_distance_matrix" fileName="snp_distance_matrix.txt"/>
</outputs>
<toolRepositories>
<repository>
<name>snippy</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>3fe8ef358d66</revision>
</repository>
<repository>
<name>gubbins</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>637ec5d5368c</revision>
</repository>
<repository>
<name>snp_sites</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>5804f786060d</revision>
</repository>
<repository>
<name>snp_dists</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>1959cc43b414</revision>
</repository>
<repository>
<name>iqtree</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>f97743d52b87</revision>
</repository>
</toolRepositories>
</iridaWorkflow>
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