{
"cwlVersion": "v1.0",
"$graph": [
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"label": "qiime2 DADA2 detect/correct paired sequence data",
"doc": "Option 1: DADA2 from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/",
"inputs": [
{
"type": "string",
"default": "stats.qza",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoising_stats_filename"
},
{
"type": "string",
"default": "rep-seqs.qza",
"id": "#qiime2-03-dada2-paired.cwl/dada2_representative_sequences_filename"
},
{
"type": "string",
"default": "stats.qzv",
"id": "#qiime2-03-dada2-paired.cwl/dada2_stats_filename"
},
{
"type": "string",
"default": "table.qza",
"id": "#qiime2-03-dada2-paired.cwl/dada2_table_filename"
},
{
"type": "File",
"id": "#qiime2-03-dada2-paired.cwl/demux_sequences_artifact"
},
{
"type": "int",
"id": "#qiime2-03-dada2-paired.cwl/n_threads"
},
{
"type": "int",
"id": "#qiime2-03-dada2-paired.cwl/trim_left_f"
},
{
"type": "int",
"id": "#qiime2-03-dada2-paired.cwl/trim_left_r"
},
{
"type": "int",
"id": "#qiime2-03-dada2-paired.cwl/trunc_len_f"
},
{
"type": "int",
"id": "#qiime2-03-dada2-paired.cwl/trunc_len_r"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/denoising_stats",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoising_stats"
},
{
"type": "File",
"outputSource": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/representative_sequences",
"id": "#qiime2-03-dada2-paired.cwl/dada2_representative_sequences"
},
{
"type": "File",
"outputSource": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/table",
"id": "#qiime2-03-dada2-paired.cwl/dada2_table"
},
{
"type": "File",
"outputSource": "#qiime2-03-dada2-paired.cwl/dada2_visualization/visualization_artifact",
"id": "#qiime2-03-dada2-paired.cwl/dada2_visualization_artifact"
}
],
"steps": [
{
"run": "#dada2-denoise-paired.cwl",
"in": [
{
"source": "#qiime2-03-dada2-paired.cwl/demux_sequences_artifact",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/demultiplexed_seqs"
},
{
"source": "#qiime2-03-dada2-paired.cwl/dada2_denoising_stats_filename",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/denoising_stats_filename"
},
{
"source": "#qiime2-03-dada2-paired.cwl/n_threads",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/n_threads"
},
{
"source": "#qiime2-03-dada2-paired.cwl/dada2_representative_sequences_filename",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/representative_sequences_filename"
},
{
"source": "#qiime2-03-dada2-paired.cwl/dada2_table_filename",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/table_filename"
},
{
"source": "#qiime2-03-dada2-paired.cwl/trim_left_f",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/trim_left_f"
},
{
"source": "#qiime2-03-dada2-paired.cwl/trim_left_r",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/trim_left_r"
},
{
"source": "#qiime2-03-dada2-paired.cwl/trunc_len_f",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/trunc_len_f"
},
{
"source": "#qiime2-03-dada2-paired.cwl/trunc_len_r",
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/trunc_len_r"
}
],
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"#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/representative_sequences",
"#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/table",
"#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/denoising_stats"
],
"id": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired"
},
{
"run": "#metadata-tabulate.cwl",
"in": [
{
"source": "#qiime2-03-dada2-paired.cwl/dada2_denoise_paired/denoising_stats",
"id": "#qiime2-03-dada2-paired.cwl/dada2_visualization/input_file"
},
{
"source": "#qiime2-03-dada2-paired.cwl/dada2_stats_filename",
"id": "#qiime2-03-dada2-paired.cwl/dada2_visualization/visualization_filename"
}
],
"out": [
"#qiime2-03-dada2-paired.cwl/dada2_visualization/visualization_artifact"
],
"id": "#qiime2-03-dada2-paired.cwl/dada2_visualization"
}
],
"id": "#qiime2-03-dada2-paired.cwl"
},
{
"class": "Workflow",
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{
"class": "SubworkflowFeatureRequirement"
}
],
"label": "qiime2 create feature visual summaries",
"doc": "FeatureTable and FeatureData summaries from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/",
"inputs": [
{
"type": "File",
"id": "#qiime2-04-features.cwl/feature_table_artifact"
},
{
"type": "string",
"default": "table.qzv",
"id": "#qiime2-04-features.cwl/feature_table_summary_filename"
},
{
"type": "string",
"default": "rep-seqs.qzv",
"id": "#qiime2-04-features.cwl/feature_table_tabulation_filename"
},
{
"type": "string",
"id": "#qiime2-04-features.cwl/filter_feature_table_where"
},
{
"type": "string",
"default": "filtered-table.qza",
"id": "#qiime2-04-features.cwl/filtered_table_filename_filename"
},
{
"type": "File",
"id": "#qiime2-04-features.cwl/rep_seqs_artifact"
},
{
"type": "File",
"id": "#qiime2-04-features.cwl/sample_metadata"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#qiime2-04-features.cwl/feature_table_summarize/visualization",
"id": "#qiime2-04-features.cwl/feature_table_summarize_visualization"
},
{
"type": "File",
"outputSource": "#qiime2-04-features.cwl/feature_table_tabulation/visualization",
"id": "#qiime2-04-features.cwl/feature_table_tabulation_visualization"
},
{
"type": "File",
"outputSource": "#qiime2-04-features.cwl/filter_feature_table/filtered_table",
"id": "#qiime2-04-features.cwl/filtered_feature_table_artifact"
}
],
"steps": [
{
"run": "#feature-table-summarize.cwl",
"in": [
{
"source": "#qiime2-04-features.cwl/sample_metadata",
"id": "#qiime2-04-features.cwl/feature_table_summarize/sample_metadata_file"
},
{
"source": "#qiime2-04-features.cwl/filter_feature_table/filtered_table",
"id": "#qiime2-04-features.cwl/feature_table_summarize/table"
},
{
"source": "#qiime2-04-features.cwl/feature_table_summary_filename",
"id": "#qiime2-04-features.cwl/feature_table_summarize/visualization_filename"
}
],
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"#qiime2-04-features.cwl/feature_table_summarize/visualization"
],
"id": "#qiime2-04-features.cwl/feature_table_summarize"
},
{
"run": "#feature-table-tabulate-seqs.cwl",
"in": [
{
"source": "#qiime2-04-features.cwl/rep_seqs_artifact",
"id": "#qiime2-04-features.cwl/feature_table_tabulation/data"
},
{
"source": "#qiime2-04-features.cwl/feature_table_tabulation_filename",
"id": "#qiime2-04-features.cwl/feature_table_tabulation/visualization_filename"
}
],
"out": [
"#qiime2-04-features.cwl/feature_table_tabulation/visualization"
],
"id": "#qiime2-04-features.cwl/feature_table_tabulation"
},
{
"run": "#feature-table-filter-samples.cwl",
"in": [
{
"source": "#qiime2-04-features.cwl/filter_feature_table_where",
"id": "#qiime2-04-features.cwl/filter_feature_table/filter_where"
},
{
"source": "#qiime2-04-features.cwl/filtered_table_filename_filename",
"id": "#qiime2-04-features.cwl/filter_feature_table/filtered_table_filename"
},
{
"source": "#qiime2-04-features.cwl/sample_metadata",
"id": "#qiime2-04-features.cwl/filter_feature_table/sample_metadata_file"
},
{
"source": "#qiime2-04-features.cwl/feature_table_artifact",
"id": "#qiime2-04-features.cwl/filter_feature_table/table"
}
],
"out": [
"#qiime2-04-features.cwl/filter_feature_table/filtered_table"
],
"id": "#qiime2-04-features.cwl/filter_feature_table"
}
],
"id": "#qiime2-04-features.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"label": "qiime2 create phylogenetic tree",
"doc": "Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/",
"inputs": [
{
"type": "string",
"default": "aligned-rep-seqs.qza",
"id": "#qiime2-05-phylogeny.cwl/aligned_rep_seqs_filename"
},
{
"type": "string",
"default": "masked-aligned-rep-seqs.qza",
"id": "#qiime2-05-phylogeny.cwl/masked_aligned_rep_seqs_filename"
},
{
"type": "File",
"id": "#qiime2-05-phylogeny.cwl/representative_sequences"
},
{
"type": "string",
"default": "rooted-tree.qza",
"id": "#qiime2-05-phylogeny.cwl/rooted_tree_filename"
},
{
"type": "string",
"default": "unrooted-tree.qza",
"id": "#qiime2-05-phylogeny.cwl/unrooted_tree_filename"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#qiime2-05-phylogeny.cwl/align_representative_sequences/alignment",
"id": "#qiime2-05-phylogeny.cwl/aligned_representative_sequences"
},
{
"type": "File",
"outputSource": "#qiime2-05-phylogeny.cwl/mask_representative_sequences/masked_aligned_rep_seqs",
"id": "#qiime2-05-phylogeny.cwl/masked_representative_sequences"
},
{
"type": "File",
"outputSource": "#qiime2-05-phylogeny.cwl/root_tree/rooted_tree",
"id": "#qiime2-05-phylogeny.cwl/rooted_tree"
},
{
"type": "File",
"outputSource": "#qiime2-05-phylogeny.cwl/create_tree_from_alignment/unrooted_tree",
"id": "#qiime2-05-phylogeny.cwl/unrooted_tree"
}
],
"steps": [
{
"run": "#alignment-mafft.cwl",
"in": [
{
"source": "#qiime2-05-phylogeny.cwl/aligned_rep_seqs_filename",
"id": "#qiime2-05-phylogeny.cwl/align_representative_sequences/alignment_filename"
},
{
"source": "#qiime2-05-phylogeny.cwl/representative_sequences",
"id": "#qiime2-05-phylogeny.cwl/align_representative_sequences/sequences"
}
],
"out": [
"#qiime2-05-phylogeny.cwl/align_representative_sequences/alignment"
],
"id": "#qiime2-05-phylogeny.cwl/align_representative_sequences"
},
{
"run": "#phylogeny-fasttree.cwl",
"in": [
{
"source": "#qiime2-05-phylogeny.cwl/mask_representative_sequences/masked_aligned_rep_seqs",
"id": "#qiime2-05-phylogeny.cwl/create_tree_from_alignment/alignment"
},
{
"source": "#qiime2-05-phylogeny.cwl/unrooted_tree_filename",
"id": "#qiime2-05-phylogeny.cwl/create_tree_from_alignment/tree_filename"
}
],
"out": [
"#qiime2-05-phylogeny.cwl/create_tree_from_alignment/unrooted_tree"
],
"id": "#qiime2-05-phylogeny.cwl/create_tree_from_alignment"
},
{
"run": "#alignment-mask.cwl",
"in": [
{
"source": "#qiime2-05-phylogeny.cwl/align_representative_sequences/alignment",
"id": "#qiime2-05-phylogeny.cwl/mask_representative_sequences/alignment"
},
{
"source": "#qiime2-05-phylogeny.cwl/masked_aligned_rep_seqs_filename",
"id": "#qiime2-05-phylogeny.cwl/mask_representative_sequences/masked_aligned_rep_seqs_filename"
}
],
"out": [
"#qiime2-05-phylogeny.cwl/mask_representative_sequences/masked_aligned_rep_seqs"
],
"id": "#qiime2-05-phylogeny.cwl/mask_representative_sequences"
},
{
"run": "#phylogeny-midpoint-root.cwl",
"in": [
{
"source": "#qiime2-05-phylogeny.cwl/rooted_tree_filename",
"id": "#qiime2-05-phylogeny.cwl/root_tree/rooted_tree_filename"
},
{
"source": "#qiime2-05-phylogeny.cwl/create_tree_from_alignment/unrooted_tree",
"id": "#qiime2-05-phylogeny.cwl/root_tree/tree"
}
],
"out": [
"#qiime2-05-phylogeny.cwl/root_tree/rooted_tree"
],
"id": "#qiime2-05-phylogeny.cwl/root_tree"
}
],
"id": "#qiime2-05-phylogeny.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
},
{
"class": "StepInputExpressionRequirement"
}
],
"label": "qiime2 explore sample taxonomic composition",
"doc": "Taxonomic analysis from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/",
"inputs": [
{
"type": "File",
"id": "#qiime2-08-taxonomic-analysis.cwl/classifier"
},
{
"type": "File",
"id": "#qiime2-08-taxonomic-analysis.cwl/rep_seqs"
},
{
"type": "File",
"id": "#qiime2-08-taxonomic-analysis.cwl/sample_metadata"
},
{
"type": "File",
"id": "#qiime2-08-taxonomic-analysis.cwl/table"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#qiime2-08-taxonomic-analysis.cwl/taxa_barplot/taxa_bar_plots",
"id": "#qiime2-08-taxonomic-analysis.cwl/taxa_barplot_file"
},
{
"type": "File",
"outputSource": "#qiime2-08-taxonomic-analysis.cwl/classify_features/out_taxa",
"id": "#qiime2-08-taxonomic-analysis.cwl/taxonomy_artifact"
},
{
"type": "File",
"outputSource": "#qiime2-08-taxonomic-analysis.cwl/tabulate_metadata/visualization_artifact",
"id": "#qiime2-08-taxonomic-analysis.cwl/taxonomy_visualization_file"
}
],
"steps": [
{
"run": "#feature-classifier-classify-sklearn.cwl",
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{
"source": "#qiime2-08-taxonomic-analysis.cwl/classifier",
"id": "#qiime2-08-taxonomic-analysis.cwl/classify_features/classifier"
},
{
"source": "#qiime2-08-taxonomic-analysis.cwl/rep_seqs",
"id": "#qiime2-08-taxonomic-analysis.cwl/classify_features/rep_seqs"
},
{
"valueFrom": "taxonomy.qza",
"id": "#qiime2-08-taxonomic-analysis.cwl/classify_features/taxonomy_filename"
}
],
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"#qiime2-08-taxonomic-analysis.cwl/classify_features/out_taxa"
],
"id": "#qiime2-08-taxonomic-analysis.cwl/classify_features"
},
{
"run": "#metadata-tabulate.cwl",
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{
"source": "#qiime2-08-taxonomic-analysis.cwl/classify_features/out_taxa",
"id": "#qiime2-08-taxonomic-analysis.cwl/tabulate_metadata/input_file"
},
{
"valueFrom": "taxonomy.qzv",
"id": "#qiime2-08-taxonomic-analysis.cwl/tabulate_metadata/visualization_filename"
}
],
"out": [
"#qiime2-08-taxonomic-analysis.cwl/tabulate_metadata/visualization_artifact"
],
"id": "#qiime2-08-taxonomic-analysis.cwl/tabulate_metadata"
},
{
"run": "#taxa-barplot.cwl",
"in": [
{
"source": "#qiime2-08-taxonomic-analysis.cwl/sample_metadata",
"id": "#qiime2-08-taxonomic-analysis.cwl/taxa_barplot/sample_metadata"
},
{
"source": "#qiime2-08-taxonomic-analysis.cwl/table",
"id": "#qiime2-08-taxonomic-analysis.cwl/taxa_barplot/table"
},
{
"valueFrom": "taxa-bar-plots.qzv",
"id": "#qiime2-08-taxonomic-analysis.cwl/taxa_barplot/taxa_bar_plots_filename"
},
{
"source": "#qiime2-08-taxonomic-analysis.cwl/classify_features/out_taxa",
"id": "#qiime2-08-taxonomic-analysis.cwl/taxa_barplot/taxonomy"
}
],
"out": [
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],
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{
"class": "CommandLineTool",
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"class": "DockerRequirement",
"dockerPull": "qiime2/core:2018.4",
"id": "#qiime2-docker-hint.yml",
"name": "#qiime2-docker-hint.yml"
}
],
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{
"type": "string",
"label": "resulting aligned sequences filename",
"inputBinding": {
"prefix": "--o-alignment"
},
"id": "#alignment-mafft.cwl/alignment_filename"
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{
"type": "File",
"label": "sequences to be aligned",
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"prefix": "--i-sequences"
},
"id": "#alignment-mafft.cwl/sequences"
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],
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"type": "File",
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"id": "#alignment-mafft.cwl/alignment"
}
],
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"mafft"
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{
"class": "CommandLineTool",
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{
"$import": "#qiime2-docker-hint.yml"
}
],
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{
"type": "File",
"label": "alignment to be masked",
"inputBinding": {
"prefix": "--i-alignment"
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{
"type": "string",
"label": "masked alignment filename",
"inputBinding": {
"prefix": "--o-masked-alignment"
},
"id": "#alignment-mask.cwl/masked_aligned_rep_seqs_filename"
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],
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{
"type": "File",
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"glob": "$(inputs.masked_aligned_rep_seqs_filename)"
},
"id": "#alignment-mask.cwl/masked_aligned_rep_seqs"
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],
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"alignment",
"mask"
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{
"class": "CommandLineTool",
"label": "qiime2: Ddenoises paired-end sequences, dereplicates them, and filters chimeras",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "File",
"label": "single-end demultiplexed sequences to be denoised",
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"prefix": "--i-demultiplexed-seqs"
},
"id": "#dada2-denoise-paired.cwl/demultiplexed_seqs"
},
{
"type": "string",
"label": "denoising stats filename",
"inputBinding": {
"prefix": "--o-denoising-stats"
},
"id": "#dada2-denoise-paired.cwl/denoising_stats_filename"
},
{
"type": "int",
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"inputBinding": {
"prefix": "--p-n-threads"
},
"id": "#dada2-denoise-paired.cwl/n_threads"
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{
"type": "string",
"label": "resulting feature sequences filename",
"inputBinding": {
"prefix": "--o-representative-sequences"
},
"id": "#dada2-denoise-paired.cwl/representative_sequences_filename"
},
{
"type": "string",
"label": "resulting feature table filename",
"inputBinding": {
"prefix": "--o-table"
},
"id": "#dada2-denoise-paired.cwl/table_filename"
},
{
"type": "int",
"label": "",
"inputBinding": {
"prefix": "--p-trim-left-f"
},
"id": "#dada2-denoise-paired.cwl/trim_left_f"
},
{
"type": "int",
"label": "",
"inputBinding": {
"prefix": "--p-trim-left-r"
},
"id": "#dada2-denoise-paired.cwl/trim_left_r"
},
{
"type": "int",
"label": "",
"inputBinding": {
"prefix": "--p-trunc-len-f"
},
"id": "#dada2-denoise-paired.cwl/trunc_len_f"
},
{
"type": "int",
"label": "",
"inputBinding": {
"prefix": "--p-trunc-len-r"
},
"id": "#dada2-denoise-paired.cwl/trunc_len_r"
}
],
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{
"type": "File",
"outputBinding": {
"glob": "$(inputs.denoising_stats_filename)"
},
"id": "#dada2-denoise-paired.cwl/denoising_stats"
},
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.representative_sequences_filename)"
},
"id": "#dada2-denoise-paired.cwl/representative_sequences"
},
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.table_filename)"
},
"id": "#dada2-denoise-paired.cwl/table"
}
],
"baseCommand": [
"qiime",
"dada2",
"denoise-paired"
],
"id": "#dada2-denoise-paired.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Classify reads by taxon using a fitted classifier",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"inputBinding": {
"prefix": "--i-classifier"
},
"label": "The taxonomic classifier for classifying the reads",
"type": "File",
"id": "#feature-classifier-classify-sklearn.cwl/classifier"
},
{
"inputBinding": {
"prefix": "--i-reads"
},
"label": "The feature data to be classified",
"type": "File",
"id": "#feature-classifier-classify-sklearn.cwl/rep_seqs"
},
{
"inputBinding": {
"prefix": "--o-classification"
},
"label": "Resulting taxonomy filename",
"type": "string",
"default": "taxonomy.qza",
"id": "#feature-classifier-classify-sklearn.cwl/taxonomy_filename"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.taxonomy_filename)"
},
"id": "#feature-classifier-classify-sklearn.cwl/out_taxa"
}
],
"baseCommand": [
"qiime",
"feature-classifier",
"classify-sklearn"
],
"id": "#feature-classifier-classify-sklearn.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Filter samples from table based on frequency and/or metadata",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "string",
"label": "Filter string to filter samples by",
"default": "BodySite='gut'",
"inputBinding": {
"prefix": "--p-where"
},
"id": "#feature-table-filter-samples.cwl/filter_where"
},
{
"type": "string",
"label": "resulting filtered table filename",
"inputBinding": {
"prefix": "--o-filtered-table"
},
"id": "#feature-table-filter-samples.cwl/filtered_table_filename"
},
{
"type": "File",
"label": "metadata file or artifact viewable as metadata",
"inputBinding": {
"prefix": "--m-metadata-file"
},
"id": "#feature-table-filter-samples.cwl/sample_metadata_file"
},
{
"type": "File",
"label": "feature table to be summarized",
"inputBinding": {
"prefix": "--i-table"
},
"id": "#feature-table-filter-samples.cwl/table"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.filtered_table_filename)"
},
"id": "#feature-table-filter-samples.cwl/filtered_table"
}
],
"baseCommand": [
"qiime",
"feature-table",
"filter-samples"
],
"id": "#feature-table-filter-samples.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Generate visual and tabular summaries of a feature table",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "File",
"label": "metadata file or artifact viewable as metadata",
"inputBinding": {
"prefix": "--m-sample-metadata-file"
},
"id": "#feature-table-summarize.cwl/sample_metadata_file"
},
{
"type": "File",
"label": "feature table to be summarized",
"inputBinding": {
"prefix": "--i-table"
},
"id": "#feature-table-summarize.cwl/table"
},
{
"type": "string",
"label": "filename for the resulting visualization file",
"inputBinding": {
"prefix": "--o-visualization"
},
"id": "#feature-table-summarize.cwl/visualization_filename"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.visualization_filename)"
},
"id": "#feature-table-summarize.cwl/visualization"
}
],
"baseCommand": [
"qiime",
"feature-table",
"summarize"
],
"id": "#feature-table-summarize.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "File",
"label": "feature sequences to be tabulated",
"inputBinding": {
"prefix": "--i-data"
},
"id": "#feature-table-tabulate-seqs.cwl/data"
},
{
"type": "string",
"label": "filename for the resulting visualization file",
"inputBinding": {
"prefix": "--o-visualization"
},
"id": "#feature-table-tabulate-seqs.cwl/visualization_filename"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.visualization_filename)"
},
"id": "#feature-table-tabulate-seqs.cwl/visualization"
}
],
"baseCommand": [
"qiime",
"feature-table",
"tabulate-seqs"
],
"id": "#feature-table-tabulate-seqs.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Generate a tabular view of metadata",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "File",
"label": "metadata file or artifact viewable as metadata",
"inputBinding": {
"prefix": "--m-input-file"
},
"id": "#metadata-tabulate.cwl/input_file"
},
{
"type": "string",
"label": "filename for the resulting visualization file",
"inputBinding": {
"prefix": "--o-visualization"
},
"id": "#metadata-tabulate.cwl/visualization_filename"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.visualization_filename)"
},
"id": "#metadata-tabulate.cwl/visualization_artifact"
}
],
"baseCommand": [
"qiime",
"metadata",
"tabulate"
],
"id": "#metadata-tabulate.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Construct a phylogenetic tree with FastTree",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "File",
"label": "aligned sequences to be used for phylogenetic reconstruction",
"inputBinding": {
"prefix": "--i-alignment"
},
"id": "#phylogeny-fasttree.cwl/alignment"
},
{
"type": "string",
"label": "resulting phylogenetic tree filename",
"inputBinding": {
"prefix": "--o-tree"
},
"id": "#phylogeny-fasttree.cwl/tree_filename"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.tree_filename)"
},
"id": "#phylogeny-fasttree.cwl/unrooted_tree"
}
],
"baseCommand": [
"qiime",
"phylogeny",
"fasttree"
],
"id": "#phylogeny-fasttree.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Midpoint root an unrooted phylogenetic tree",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "string",
"label": "rooted phylogenetic tree",
"inputBinding": {
"prefix": "--o-rooted-tree"
},
"id": "#phylogeny-midpoint-root.cwl/rooted_tree_filename"
},
{
"type": "File",
"label": "phylogenetic tree to be rooted",
"inputBinding": {
"prefix": "--i-tree"
},
"id": "#phylogeny-midpoint-root.cwl/tree"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.rooted_tree_filename)"
},
"id": "#phylogeny-midpoint-root.cwl/rooted_tree"
}
],
"baseCommand": [
"qiime",
"phylogeny",
"midpoint-root"
],
"id": "#phylogeny-midpoint-root.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Produce an interactive barplot visualization of taxonomies",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "File",
"label": "Metadata file or artifact viewable as metadata",
"inputBinding": {
"prefix": "--m-metadata-file"
},
"id": "#taxa-barplot.cwl/sample_metadata"
},
{
"type": "File",
"label": "Feature table to visualize at various taxonomic levels",
"inputBinding": {
"prefix": "--i-table"
},
"id": "#taxa-barplot.cwl/table"
},
{
"type": "string",
"label": "The resulting visualization filename",
"inputBinding": {
"prefix": "--o-visualization"
},
"id": "#taxa-barplot.cwl/taxa_bar_plots_filename"
},
{
"type": "File",
"label": "Taxonomic annotations for features in the provided feature table",
"inputBinding": {
"prefix": "--i-taxonomy"
},
"id": "#taxa-barplot.cwl/taxonomy"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.taxa_bar_plots_filename)"
},
"id": "#taxa-barplot.cwl/taxa_bar_plots"
}
],
"baseCommand": [
"qiime",
"taxa",
"barplot"
],
"id": "#taxa-barplot.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"label": "QIIME2 Step 2 (DADA2 option)",
"doc": "QIIME2 DADA2, feature summaries, phylogenetic diversity tree, taxonomic analysis and ancom\n",
"inputs": [
{
"type": "int",
"id": "#main/dada2_denoise_n_threads"
},
{
"type": "int",
"id": "#main/dada2_trim_left_f"
},
{
"type": "int",
"id": "#main/dada2_trim_left_r"
},
{
"type": "int",
"id": "#main/dada2_trunc_len_f"
},
{
"type": "int",
"id": "#main/dada2_trunc_len_r"
},
{
"type": "File",
"id": "#main/demux_sequences_artifact"
},
{
"type": "string",
"id": "#main/filter_feature_table_where"
},
{
"type": "File",
"id": "#main/sample_metadata"
},
{
"type": "File",
"id": "#main/taxonomic_classifier"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#main/phylogenetic_tree/aligned_representative_sequences",
"id": "#main/aligned_representative_sequences"
},
{
"type": "File",
"outputSource": "#main/dada2_sequences/dada2_denoising_stats",
"id": "#main/dada2_denoising_stats"
},
{
"type": "File",
"outputSource": "#main/dada2_sequences/dada2_representative_sequences",
"id": "#main/dada2_representative_sequences"
},
{
"type": "File",
"outputSource": "#main/dada2_sequences/dada2_table",
"id": "#main/dada2_table"
},
{
"type": "File",
"outputSource": "#main/dada2_sequences/dada2_visualization_artifact",
"id": "#main/dada2_visualization_artifact"
},
{
"type": "File",
"outputSource": "#main/feature_table_visualizations/feature_table_summarize_visualization",
"id": "#main/feature_table_summarize_visualization"
},
{
"type": "File",
"outputSource": "#main/feature_table_visualizations/feature_table_tabulation_visualization",
"id": "#main/feature_table_tabulation_visualization"
},
{
"type": "File",
"outputSource": "#main/feature_table_visualizations/filtered_feature_table_artifact",
"id": "#main/filtered_feature_table_artifact"
},
{
"type": "File",
"outputSource": "#main/phylogenetic_tree/masked_representative_sequences",
"id": "#main/masked_representative_sequences"
},
{
"type": "File",
"outputSource": "#main/phylogenetic_tree/rooted_tree",
"id": "#main/rooted_tree"
},
{
"type": "File",
"outputSource": "#main/taxonomic_analysis/taxa_barplot_file",
"id": "#main/taxa_barplot_file"
},
{
"type": "File",
"outputSource": "#main/taxonomic_analysis/taxonomy_artifact",
"id": "#main/taxonomy_artifact"
},
{
"type": "File",
"outputSource": "#main/taxonomic_analysis/taxonomy_visualization_file",
"id": "#main/taxonomy_visualization_file"
},
{
"type": "File",
"outputSource": "#main/phylogenetic_tree/unrooted_tree",
"id": "#main/unrooted_tree"
}
],
"steps": [
{
"run": "#qiime2-03-dada2-paired.cwl",
"in": [
{
"source": "#main/demux_sequences_artifact",
"id": "#main/dada2_sequences/demux_sequences_artifact"
},
{
"source": "#main/dada2_denoise_n_threads",
"id": "#main/dada2_sequences/n_threads"
},
{
"source": "#main/dada2_trim_left_f",
"id": "#main/dada2_sequences/trim_left_f"
},
{
"source": "#main/dada2_trim_left_r",
"id": "#main/dada2_sequences/trim_left_r"
},
{
"source": "#main/dada2_trunc_len_f",
"id": "#main/dada2_sequences/trunc_len_f"
},
{
"source": "#main/dada2_trunc_len_r",
"id": "#main/dada2_sequences/trunc_len_r"
}
],
"out": [
"#main/dada2_sequences/dada2_representative_sequences",
"#main/dada2_sequences/dada2_table",
"#main/dada2_sequences/dada2_denoising_stats",
"#main/dada2_sequences/dada2_visualization_artifact"
],
"id": "#main/dada2_sequences"
},
{
"run": "#qiime2-04-features.cwl",
"in": [
{
"source": "#main/dada2_sequences/dada2_table",
"id": "#main/feature_table_visualizations/feature_table_artifact"
},
{
"source": "#main/filter_feature_table_where",
"id": "#main/feature_table_visualizations/filter_feature_table_where"
},
{
"source": "#main/dada2_sequences/dada2_representative_sequences",
"id": "#main/feature_table_visualizations/rep_seqs_artifact"
},
{
"source": "#main/sample_metadata",
"id": "#main/feature_table_visualizations/sample_metadata"
}
],
"out": [
"#main/feature_table_visualizations/filtered_feature_table_artifact",
"#main/feature_table_visualizations/feature_table_summarize_visualization",
"#main/feature_table_visualizations/feature_table_tabulation_visualization"
],
"id": "#main/feature_table_visualizations"
},
{
"run": "#qiime2-05-phylogeny.cwl",
"in": [
{
"source": "#main/dada2_sequences/dada2_representative_sequences",
"id": "#main/phylogenetic_tree/representative_sequences"
}
],
"out": [
"#main/phylogenetic_tree/aligned_representative_sequences",
"#main/phylogenetic_tree/masked_representative_sequences",
"#main/phylogenetic_tree/unrooted_tree",
"#main/phylogenetic_tree/rooted_tree"
],
"id": "#main/phylogenetic_tree"
},
{
"run": "#qiime2-08-taxonomic-analysis.cwl",
"in": [
{
"source": "#main/taxonomic_classifier",
"id": "#main/taxonomic_analysis/classifier"
},
{
"source": "#main/dada2_sequences/dada2_representative_sequences",
"id": "#main/taxonomic_analysis/rep_seqs"
},
{
"source": "#main/sample_metadata",
"id": "#main/taxonomic_analysis/sample_metadata"
},
{
"source": "#main/dada2_sequences/dada2_table",
"id": "#main/taxonomic_analysis/table"
}
],
"out": [
"#main/taxonomic_analysis/taxonomy_artifact",
"#main/taxonomic_analysis/taxonomy_visualization_file",
"#main/taxonomic_analysis/taxa_barplot_file"
],
"id": "#main/taxonomic_analysis"
}
],
"id": "#main"
}
]
}