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bumped up the version with sed
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@zipho
zipho committed Sep 14, 2020
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4 changes: 2 additions & 2 deletions tb-sample-report-pipeline-plugin/pom.xml
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<modelVersion>4.0.0</modelVersion>
<groupId>ca.corefacility.bioinformatics.irida.plugins</groupId>
<artifactId>tb-sample-report-pipeline-plugin</artifactId>
<version>0.2.2-SNAPSHOT</version>
<version>0.2.3-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>tb-sample-report-pipeline-plugin</plugin.id>
<plugin.class>ca.corefacility.bioinformatics.irida.plugins.SnippyPipelinePlugin</plugin.class>
<plugin.version>0.2.2</plugin.version>
<plugin.version>0.2.3</plugin.version>
<plugin.provider>COMBAT-TB</plugin.provider>
<plugin.dependencies></plugin.dependencies>
<plugin.requires.runtime>1.0.0</plugin.requires.runtime>
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184 changes: 184 additions & 0 deletions tb-sample-report-pipeline-plugin/src/main/resources/workflows/0.2.3/irida_workflow.xml
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<?xml version="1.0" encoding="UTF-8"?>
<iridaWorkflow>
<id>174a2e3a-409c-49bb-9737-337646801b00</id>
<name>TBSampleReport</name>
<version>0.2.3</version>
<analysisType>VARIANT_CALLING</analysisType>
<inputs>
<sequenceReadsPaired>sequence_input</sequenceReadsPaired>
<reference>reference</reference>
<requiresSingleSample>true</requiresSingleSample>
</inputs>
<parameters>
<parameter name="text_processing-2-name" defaultValue="sed_reference">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1" parameterName="name"/>
</parameter>
<parameter name="text_processing-2-adv_opts.adv_opts_selector" defaultValue="basic">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1" parameterName="adv_opts.adv_opts_selector"/>
</parameter>
<parameter name="text_processing-2-code" defaultValue="s/^&gt;/&gt;Chromosome/">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1" parameterName="code" label="AWK Program" type="text"/>
</parameter>
<parameter name="fastqc-3-chromInfo" defaultValue="/opt/galaxy/tool-data/shared/ucsc/chrom/?.len">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1" parameterName="chromInfo"/>
</parameter>
<parameter name="fastqc-3-min_length" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1" parameterName="min_length"/>
</parameter>
<parameter name="trimmomatic-4-illuminaclip.do_illuminaclip" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1" parameterName="illuminaclip.do_illuminaclip" label="Perform initial ILLUMINACLIP step?" type="boolean"/>
</parameter>
<parameter name="trimmomatic-4-readtype.single_or_paired" defaultValue="collection">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1" parameterName="readtype.single_or_paired" label="Single-end or paired-end reads?" type="select"/>
</parameter>
<parameter name="snippy-5-adv.minfrac" defaultValue="0.1">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="adv.minfrac"/>
</parameter>
<parameter name="snippy-5-adv.mincov" defaultValue="10">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="adv.mincov"/>
</parameter>
<parameter name="snippy-5-adv.rgid" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="adv.rgid"/>
</parameter>
<parameter name="snippy-5-adv.rename_cons" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="adv.rename_cons"/>
</parameter>
<parameter name="snippy-5-adv.mapqual" defaultValue="60">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="adv.mapqual"/>
</parameter>
<parameter name="snippy-5-adv.bwaopt" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="adv.bwaopt"/>
</parameter>
<parameter name="snippy-5-reference_source.reference_source_selector" defaultValue="history">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="reference_source.reference_source_selector"/>
</parameter>
<parameter name="snippy-5-fastq_input.fastq_input_selector" defaultValue="paired_collection">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="fastq_input.fastq_input_selector"/>
</parameter>
<parameter name="snippy-5-adv.minqual" defaultValue="100.0">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0" parameterName="adv.minqual"/>
</parameter>
<parameter name="snpeff-6-chr" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="chr"/>
</parameter>
<parameter name="snpeff-6-offset" defaultValue="default">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="offset"/>
</parameter>
<parameter name="snpeff-6-spliceRegion.setSpliceRegions" defaultValue="no">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="spliceRegion.setSpliceRegions"/>
</parameter>
<parameter name="snpeff-6-snpDb.reg_section.regulation" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="snpDb.reg_section.regulation"/>
</parameter>
<parameter name="snpeff-6-filter.specificEffects" defaultValue="no">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="filter.specificEffects"/>
</parameter>
<parameter name="snpeff-6-snpDb.genomeSrc" defaultValue="cached">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="snpDb.genomeSrc"/>
</parameter>
<parameter name="snpeff-6-inputFormat" defaultValue="vcf">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="inputFormat"/>
</parameter>
<parameter name="snpeff-6-snpDb.genomeVersion" defaultValue="Mycobacterium_tuberculosis_h37rv">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="snpDb.genomeVersion"/>
</parameter>
<parameter name="snpeff-6-outputConditional.outputFormat" defaultValue="vcf">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1" parameterName="outputConditional.outputFormat"/>
</parameter>
<parameter name="tbprofiler-7-advanced.mapper" defaultValue="bwa">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="advanced.mapper"/>
</parameter>
<parameter name="tbprofiler-7-output_format" defaultValue="txt">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="output_format"/>
</parameter>
<parameter name="tbprofiler-7-chromInfo" defaultValue="/opt/galaxy/tool-data/shared/ucsc/chrom/?.len">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="chromInfo"/>
</parameter>
<parameter name="tbprofiler-7-fastq_or_bam.input_select" defaultValue="bam">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="fastq_or_bam.input_select"/>
</parameter>
<parameter name="tbprofiler-7-advanced.min_allele_freq" defaultValue="0.1">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="advanced.min_allele_freq"/>
</parameter>
<parameter name="tbprofiler-7-advanced.min_allele_freq_reporting" defaultValue="0.1">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="advanced.min_allele_freq_reporting"/>
</parameter>
<parameter name="tbprofiler-7-advanced.options" defaultValue="yes">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="advanced.options"/>
</parameter>
<parameter name="tbprofiler-7-platform" defaultValue="illumina">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="platform"/>
</parameter>
<parameter name="tbprofiler-7-advanced.min_depth" defaultValue="10">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" parameterName="advanced.min_depth"/>
</parameter>
<parameter name="tb_variant_filter-8-chromInfo" defaultValue="/opt/galaxy/tool-data/shared/ucsc/chrom/?.len">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0" parameterName="chromInfo"/>
</parameter>
<parameter name="tb_variant_filter-8-filter_options.show_filter_options" defaultValue="no">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0" parameterName="filter_options.show_filter_options"/>
</parameter>
<parameter name="tbvcfreport-9-adv.database_uri" defaultValue="neodb.sanbi.ac.za">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/0.1.7+galaxy0" parameterName="adv.database_uri" label="Specify on-premise COMBAT-TB-NeoDB URI" type="text"/>
</parameter>
</parameters>
<outputs>
<output name="sed_reference" fileName="sed_reference"/>
<output name="snpeff_output" fileName="snpeff_output" />
<output name="output1" fileName="output1" />
<output name="variants_report_html" fileName="variants_report_html" />
<output name="variants_report_txt" fileName="variants_report_txt" />
<output name="drug_resistance_report_html" fileName="drug_resistance_report_html" />
<output name="drug_resistance_report_txt" fileName="drug_resistance_report_txt" />
</outputs>
<toolRepositories>
<repository>
<name>trimmomatic</name>
<owner>pjbriggs</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>d94aff5ee623</revision>
</repository>
<repository>
<name>tbprofiler</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>200c378d85f3</revision>
</repository>
<repository>
<name>snpeff</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>268d162b9c49</revision>
</repository>
<repository>
<name>fastqc</name>
<owner>devteam</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>e7b2202befea</revision>
</repository>
<repository>
<name>tbvcfreport</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>02d81b994ef5</revision>
</repository>
<repository>
<name>tb_variant_filter</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>3b1e7c170b10</revision>
</repository>
<repository>
<name>snippy</name>
<owner>iuc</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>5bbf9eada9c2</revision>
</repository>
<repository>
<name>text_processing</name>
<owner>bgruening</owner>
<url>https://toolshed.g2.bx.psu.edu</url>
<revision>0a8c6b61f0f4</revision>
</repository>
</toolRepositories>
</iridaWorkflow>
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