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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/^>/>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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