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Add workflow version 0.1.1 with fix for iqtree short alignments (#5)
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<?xml version="1.0" encoding="UTF-8"?> | ||
<iridaWorkflow> | ||
<id>bd535929-cef1-4d03-9354-61e0d43945d9</id> | ||
<name>snippy-phylogenomics</name> | ||
<version>0.1.1</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="distance_matrix" fileName="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>iqtree</name> | ||
<owner>iuc</owner> | ||
<url>https://toolshed.g2.bx.psu.edu</url> | ||
<revision>f97743d52b87</revision> | ||
</repository> | ||
</toolRepositories> | ||
</iridaWorkflow> |
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