{"@id":"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl","retrievedFrom":{"repoUrl":"https://github.com/MG-RAST/qiime-pipeline.git","branch":"ea3f99c0fc58d161e068bd5077c362768e534b92","path":"CWL/Workflows/qiime/cluster2plot.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/MG-RAST/qiime-pipeline/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl","url":"https://github.com/MG-RAST/qiime-pipeline/blob/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl"},"retrievedOn":"2026-08-26T05:26:54.184+00:00","lastCommit":"ea3f99c0fc58d161e068bd5077c362768e534b92","label":"fasta2taxa-plot","doc":"Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file.\nThe workflow calls open otus and assigns taxa using greengenes. The output are taxa plots. \n","inputs":{"sample-mapping":{"type":"File"},"fasta-demultiplexed":{"type":"File"},"min-observations-per-otu":{"type":"Integer (Optional)"},"min-observations-per-sample":{"type":"Integer (Optional)"},"summarize-for-taxonomic-levels":{}},"outputs":{"results":{"type":"Directory[]"},"error-logs":{"doc":"Error logs for each step, collected by default and can be empty.","type":"File[]"},"taxa-summary-plots":{"type":"Directory"},"beta-diversity-results":{"type":"Directory"},"aplha-diversity-results":{"type":"File"}},"steps":{"cluster":{"run":"../../Tools/qiime/pick_de_novo_otus.cwl","runType":"COMMANDLINETOOL","sources":{"cluster":{"sourceIDs":["fasta-demultiplexed"]}}},"taxonomy":{"run":"../../Tools/qiime/assign_taxonomy.cwl","runType":"COMMANDLINETOOL","sources":{"taxonomy":{"sourceIDs":["cluster"]}}},"otu-table":{"run":"../../Tools/qiime/make_otu_table.cwl","runType":"COMMANDLINETOOL","sources":{"otu-table":{"sourceIDs":["taxonomy"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#otu-table/otu-mapping":{"sourceIDs":["cluster"]}}},"sort-table":{"run":"../../Tools/qiime/sort_otu_table.cwl","runType":"COMMANDLINETOOL","sources":{"sort-table":{"sourceIDs":["sample-mapping"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#sort-table/otu-biom-table":{"sourceIDs":["otu-table"]}}},"filter-otus":{"run":"../../Tools/qiime/filter_otus_from_otu_table.cwl","runType":"COMMANDLINETOOL","sources":{"filter-otus":{"sourceIDs":["min-observations-per-otu"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#filter-otus/otu-biom-table":{"sourceIDs":["sort-table"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#filter-otus/min_observation_count":{"defaultVal":"2"}}},"beta-diversity":{"run":"../../Tools/qiime/beta_diversity_through_plots.cwl","runType":"COMMANDLINETOOL","sources":{"beta-diversity":{"sourceIDs":["filter-samples"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#beta-diversity/tree":{"sourceIDs":["cluster"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#beta-diversity/mapping":{"sourceIDs":["sample-mapping"]}}},"filter-samples":{"run":"../../Tools/qiime/filter_samples_from_otu_table.cwl","runType":"COMMANDLINETOOL","sources":{"filter-samples":{"sourceIDs":["min-observations-per-sample"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#filter-samples/otu-biom-table":{"sourceIDs":["filter-otus"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#filter-samples/min_observation_count":{"defaultVal":"100"}}},"summarize-taxa":{"run":"../../Tools/qiime/summarize_taxa.cwl","runType":"COMMANDLINETOOL","sources":{"summarize-taxa":{"sourceIDs":["filter-samples"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#summarize-taxa/taxonomic-level":{"sourceIDs":["summarize-for-taxonomic-levels"]}}},"alpha-diversity":{"run":"../../Tools/qiime/alpha_diversity.cwl","runType":"COMMANDLINETOOL","sources":{"alpha-diversity":{"defaultVal":"\\\"shannon\\\""},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#alpha-diversity/tree":{"sourceIDs":["cluster"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#alpha-diversity/method":{"defaultVal":"\\\"PD_whole_tree\\\""},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#alpha-diversity/otu-table":{"sourceIDs":["filter-samples"]}}},"plot-taxa-summary":{"run":"../../Tools/qiime/plot_taxa_summary.cwl","runType":"COMMANDLINETOOL","sources":{"plot-taxa-summary":{"sourceIDs":["summarize-taxa"]},"https://w3id.org/cwl/view/git/ea3f99c0fc58d161e068bd5077c362768e534b92/CWL/Workflows/qiime/cluster2plot.cwl#plot-taxa-summary/labels":{"sourceIDs":["summarize-for-taxonomic-levels"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph 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