# HG changeset patch # User florianbegusch # Date 1563347117 14400 # Node ID 370e0b6e982627ceb3ccd7c226fa1ddcb3040d48 Uploaded diff -r 000000000000 -r 370e0b6e9826 qiime2/merge_feature_table_and_taxonomy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/merge_feature_table_and_taxonomy.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,34 @@ + + + - Merge features and taxonomy into a single biom file. + + qiime2 + + +mkdir out; + +qiime tools export --input-path --output-path out $taxonomy_qza; +qiime tools export --input-path --output-path out $biom_qza; + +sed -i '1s;^;#;' out/*.tsv; +sed -i 's/Confidence/confidence/g' out/*.tsv; +sed -i 's/Taxon/taxonomy/g' out/*.tsv; +sed -i 's/Feature ID/OTU ID/g' out/*.tsv; + +biom add-metadata -i out/*.biom -o table_with_sample_metadata.biom --observation-metadata-fp out/*.tsv +; +mv *.biom $biom_and_tax_merged + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_alignment_mafft.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_alignment_mafft.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,56 @@ + + + - De novo multiple sequence alignment with MAFFT + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_alignment_mask.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_alignment_mask.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,66 @@ + + + - Positional conservation and gap filtering. + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_citation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_citation.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,24 @@ + + + + + @article{10.7287/peerj.preprints.27295v2, + title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, + author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Zhu, Qiyun and Knight, Rob and Caporaso, J Gregory}, + year = 2019, + month = dec, + keywords = {microbiome, bioinformatics, data science, software, microbial ecology, reproducibility}, + abstract = { + We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science. + }, + volume = 6, + pages = {e27295v2}, + journal = {PeerJ Preprints}, + issn = {2167-9843}, + url = {https://doi.org/10.7287/peerj.preprints.27295v2}, + doi = {10.7287/peerj.preprints.27295v2} + } + + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_composition_add-pseudocount.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_composition_add-pseudocount.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,48 @@ + + + - Add pseudocount to table + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_composition_ancom.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_composition_ancom.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,87 @@ + + + - Apply ANCOM to identify features that differ in abundance. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_cutadapt_demux-paired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_cutadapt_demux-paired.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,92 @@ + + + - Demultiplex paired-end sequence data with barcodes in- sequence. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_cutadapt_demux-single.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_cutadapt_demux-single.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,76 @@ + + + - Demultiplex single-end sequence data with barcodes in- sequence. + + qiime2 + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_cutadapt_trim-paired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_cutadapt_trim-paired.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,190 @@ + + + - Find and remove adapters in demultiplexed paired-end sequences. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_cutadapt_trim-single.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_cutadapt_trim-single.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,151 @@ + + + - Find and remove adapters in demultiplexed single-end sequences. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_dada2_denoise-paired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_dada2_denoise-paired.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,164 @@ + + + - Denoise and dereplicate paired-end sequences + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_dada2_denoise-pyro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_dada2_denoise-pyro.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,149 @@ + + + - Denoise and dereplicate single-end pyrosequences + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_dada2_denoise-single.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_dada2_denoise-single.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,140 @@ + + + - Denoise and dereplicate single-end sequences + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_deblur_denoise-16S.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_deblur_denoise-16S.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,128 @@ + + + - Deblur sequences using a 16S positive filter. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_deblur_denoise-other.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_deblur_denoise-other.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,133 @@ + + + - Deblur sequences using a user-specified positive filter. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_deblur_visualize-stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_deblur_visualize-stats.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,43 @@ + + + - Visualize Deblur stats per sample. + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_demux_emp-paired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_emp-paired.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,92 @@ + + + - Demultiplex paired-end sequence data generated with the EMP protocol. + + qiime2 + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_demux_emp-single.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_emp-single.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,93 @@ + + + - Demultiplex sequence data generated with the EMP protocol. + + qiime2 + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_demux_subsample-paired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_subsample-paired.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,50 @@ + + + - Subsample paired-end sequences without replacement. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_demux_subsample-single.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_subsample-single.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,50 @@ + + + - Subsample single-end sequences without replacement. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_demux_summarize.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_summarize.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,55 @@ + + + - Summarize counts per sample. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_adonis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_adonis.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,94 @@ + + + - adonis PERMANOVA test for beta group significance + + qiime2 + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_alpha-correlation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_alpha-correlation.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,73 @@ + + + - Alpha diversity correlation + + qiime2 + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_alpha-group-significance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_alpha-group-significance.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,69 @@ + + + - Alpha diversity comparisons + + qiime2 + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_alpha-phylogenetic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_alpha-phylogenetic.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,57 @@ + + + - Alpha diversity (phylogenetic) + + qiime2 + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_alpha-rarefaction.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_alpha-rarefaction.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,134 @@ + + + - Alpha rarefaction curves + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_alpha.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_alpha.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,79 @@ + + + - Alpha diversity + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_beta-correlation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_beta-correlation.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,116 @@ + + + - Beta diversity correlation + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_beta-group-significance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_beta-group-significance.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,95 @@ + + + - Beta diversity group significance + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_beta-phylogenetic-alt.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_beta-phylogenetic-alt.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,112 @@ + + + - Beta diversity (phylogenetic) - High Performance Computation + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_beta-phylogenetic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_beta-phylogenetic.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,97 @@ + + + - Beta diversity (phylogenetic) + + qiime2 + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_beta-rarefaction.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_beta-rarefaction.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,168 @@ + + + - Beta diversity rarefaction + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_beta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_beta.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,85 @@ + + + - Beta diversity + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_bioenv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_bioenv.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,68 @@ + + + - bioenv + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_core-metrics-phylogenetic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_core-metrics-phylogenetic.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,167 @@ + + + - Core diversity metrics (phylogenetic and non- phylogenetic) + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_core-metrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_core-metrics.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,121 @@ + + + - Core diversity metrics (non-phylogenetic) + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_filter-distance-matrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_filter-distance-matrix.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,92 @@ + + + - Filter samples from a distance matrix. + + qiime2 + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_mantel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_mantel.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,98 @@ + + + - Apply the Mantel test to two distance matrices + + qiime2 + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_pcoa-biplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_pcoa-biplot.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,49 @@ + + + - Principal Coordinate Analysis Biplot + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_pcoa.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_pcoa.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,58 @@ + + + - Principal Coordinate Analysis + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_diversity_procrustes-analysis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_procrustes-analysis.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,58 @@ + + + - Procrustes Analysis + + qiime2 + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_emperor_biplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_emperor_biplot.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,89 @@ + + + - Visualize and Interact with Principal Coordinates Analysis Biplot + + qiime2 + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_emperor_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_emperor_plot.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,83 @@ + + + - Visualize and Interact with Principal Coordinates Analysis Plots + + qiime2 + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_emperor_procrustes-plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_emperor_procrustes-plot.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,88 @@ + + + - Visualize and Interact with a procrustes plot + + qiime2 + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-classifier_classify-consensus-blast.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-classifier_classify-consensus-blast.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,140 @@ + + + - BLAST+ consensus taxonomy classifier + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + perc_identity similarity to query, not the top N +matches. For top N hits, use classify-consensus-vsearch. + +Parameters +---------- +query : FeatureData[Sequence] + Sequences to classify taxonomically. +reference_reads : FeatureData[Sequence] + reference sequences. +reference_taxonomy : FeatureData[Taxonomy] + reference taxonomy labels. +maxaccepts : Int % Range(1, None), optional + Maximum number of hits to keep for each query. Must be in range [1, + infinity]. BLAST will choose the first N hits in the reference database + that exceed perc_identity similarity to query. +perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional + Reject match if percent identity to query is lower. Must be in range + [0.0, 1.0]. +query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional + Reject match if query alignment coverage per high-scoring pair is + lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not + behave identically to the query_cov parameter used by classify- + consensus-vsearch. Must be in range [0.0, 1.0]. +strand : Str % Choices('both', 'plus', 'minus'), optional + Align against reference sequences in forward ("plus"), reverse + ("minus"), or both directions ("both"). +evalue : Float, optional + BLAST expectation value (E) threshold for saving hits. +min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional + Minimum fraction of assignments must match top hit to be accepted as + consensus assignment. Must be in range (0.5, 1.0]. +unassignable_label : Str, optional + \ + +Returns +------- +classification : FeatureData[Taxonomy] + Taxonomy classifications of query sequences. + ]]> + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,135 @@ + + + - VSEARCH consensus taxonomy classifier + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + perc_identity similarity. Must be in range [0, infinity]. +perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional + Reject match if percent identity to query is lower. Must be in range + [0.0, 1.0]. +query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional + Reject match if query alignment coverage per high-scoring pair is + lower. Must be in range [0.0, 1.0]. +strand : Str % Choices('both', 'plus'), optional + Align against reference sequences in forward ("plus") or both + directions ("both"). +min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional + Minimum fraction of assignments must match top hit to be accepted as + consensus assignment. Must be in range (0.5, 1.0]. +unassignable_label : Str, optional + \ + +Returns +------- +classification : FeatureData[Taxonomy] + The resulting taxonomy classifications. + ]]> + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-classifier_classify-sklearn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-classifier_classify-sklearn.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,81 @@ + + + - Pre-fitted sklearn-based taxonomy classifier + + qiime2 + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-classifier_extract-reads.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-classifier_extract-reads.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,91 @@ + + + - Extract reads from reference + + qiime2 + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,260 @@ + + + - Train the naive_bayes classifier + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,86 @@ + + + - Train an almost arbitrary scikit-learn classifier + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_core-features.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_core-features.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,69 @@ + + + - Identify core features in table + + qiime2 + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_filter-features.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_filter-features.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,121 @@ + + + - Filter features from table + + qiime2 + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_filter-samples.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_filter-samples.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,120 @@ + + + - Filter samples from table + + qiime2 + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_filter-seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_filter-seqs.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,97 @@ + + + - Filter features from sequences + + qiime2 + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_group.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_group.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,87 @@ + + + - Group samples or features by a metadata column + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_heatmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_heatmap.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,332 @@ + + + - Generate a heatmap representation of a feature table + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_merge-seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_merge-seqs.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,56 @@ + + + - Combine collections of feature sequences + + qiime2 + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_merge-taxa.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_merge-taxa.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,56 @@ + + + - Combine collections of feature taxonomies + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_merge.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,66 @@ + + + - Combine multiple tables + + qiime2 + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_presence-absence.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_presence-absence.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,43 @@ + + + - Convert to presence/absence + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_rarefy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_rarefy.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,58 @@ + + + - Rarefy table + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_relative-frequency.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_relative-frequency.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,43 @@ + + + - Convert to relative frequencies + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_subsample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_subsample.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,57 @@ + + + - Subsample table + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_summarize.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_summarize.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,58 @@ + + + - Summarize table + + qiime2 + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_tabulate-seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_tabulate-seqs.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,44 @@ + + + - View sequence associated with each feature + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_feature-table_transpose.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_transpose.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,43 @@ + + + - Transpose a feature table. + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_fragment-insertion_classify-otus-experimental.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_fragment-insertion_classify-otus-experimental.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,77 @@ + + + - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_fragment-insertion_filter-features.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_fragment-insertion_filter-features.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,66 @@ + + + - Filter fragments in tree from table. + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_fragment-insertion_sepp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_fragment-insertion_sepp.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,103 @@ + + + - Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8 + + qiime2 + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_add-pseudocount.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_add-pseudocount.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,55 @@ + + + - Add pseudocount to table + + qiime2 + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_assign-ids.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_assign-ids.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,53 @@ + + + - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_balance-taxonomy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_balance-taxonomy.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,111 @@ + + + - Balance Summary + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_correlation-clustering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_correlation-clustering.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,55 @@ + + + - Hierarchical clustering using feature correlation. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_dendrogram-heatmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_dendrogram-heatmap.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,187 @@ + + + - Dendrogram heatmap. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_gradient-clustering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_gradient-clustering.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,79 @@ + + + - Hierarchical clustering using gradient information. + + qiime2 + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_ilr-hierarchical.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_ilr-hierarchical.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,59 @@ + + + - Isometric Log-ratio Transform applied to a hierarchical clustering + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_ilr-phylogenetic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_ilr-phylogenetic.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,65 @@ + + + - Isometric Log-ratio Transform applied to a phylogenetic tree + + qiime2 + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_ilr-transform.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_ilr-transform.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,56 @@ + + + - Isometric Log-ratio Transform + + qiime2 + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_lme-regression.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_lme-regression.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,78 @@ + + + - Simplicial Linear mixed effects regression + + qiime2 + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_gneiss_ols-regression.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_gneiss_ols-regression.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,80 @@ + + + - Simplicial Ordinary Least Squares Regression + + qiime2 + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_anova.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_anova.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,87 @@ + + + - ANOVA test + + qiime2 + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_feature-volatility.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_feature-volatility.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,176 @@ + + + - Feature volatility analysis + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_first-differences.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_first-differences.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,116 @@ + + + - Compute first differences or difference from baseline between sequential states + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_first-distances.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_first-distances.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,109 @@ + + + - Compute first distances or distance from baseline between sequential states + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_linear-mixed-effects.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_linear-mixed-effects.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,166 @@ + + + - Linear mixed effects modeling + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_maturity-index.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_maturity-index.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,255 @@ + + + - Microbial maturity index prediction. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_nmit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_nmit.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,92 @@ + + + - Nonparametric microbial interdependence test + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_pairwise-differences.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_pairwise-differences.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,157 @@ + + + - Paired difference testing and boxplots + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_pairwise-distances.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_pairwise-distances.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,144 @@ + + + - Paired pairwise distance testing and boxplots + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_plot-feature-volatility.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_plot-feature-volatility.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,105 @@ + + + - Plot longitudinal feature volatility and importances + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_longitudinal_volatility.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_longitudinal_volatility.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,116 @@ + + + - Generate interactive volatility plot + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_metadata_distance-matrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_metadata_distance-matrix.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,62 @@ + + + - Create a distance matrix from a numeric Metadata column + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_metadata_tabulate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_metadata_tabulate.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,64 @@ + + + - Interactively explore Metadata in an HTML table + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,96 @@ + + + - Build a phylogenetic tree using fasttree and mafft alignment + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_fasttree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_fasttree.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,47 @@ + + + - Construct a phylogenetic tree with FastTree. + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_filter-table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_filter-table.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,48 @@ + + + - Remove features from table if they're not present in tree. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,503 @@ + + + - Construct a phylogenetic tree with IQ-TREE with bootstrap supports. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_iqtree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_iqtree.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,470 @@ + + + - Construct a phylogenetic tree with IQ-TREE. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_midpoint-root.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_midpoint-root.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,42 @@ + + + - Midpoint root an unrooted phylogenetic tree. + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,103 @@ + + + - Construct a phylogenetic tree with bootstrap supports using RAxML. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_phylogeny_raxml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_phylogeny_raxml.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,94 @@ + + + - Construct a phylogenetic tree with RAxML. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_quality-control_evaluate-composition.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_quality-control_evaluate-composition.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,182 @@ + + + - Evaluate expected vs. observed taxonomic composition of samples + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_quality-control_evaluate-seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_quality-control_evaluate-seqs.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,57 @@ + + + - Compare query (observed) vs. reference (expected) sequences. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_quality-control_evaluate-taxonomy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_quality-control_evaluate-taxonomy.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,122 @@ + + + - Evaluate expected vs. observed taxonomic assignments + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_quality-control_exclude-seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_quality-control_exclude-seqs.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,103 @@ + + + - Exclude sequences by alignment + + qiime2 + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_quality-filter_q-score-joined.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_quality-filter_q-score-joined.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,81 @@ + + + - Quality filter based on joined sequence quality scores. + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_quality-filter_q-score.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_quality-filter_q-score.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,81 @@ + + + - Quality filter based on sequence quality scores. + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_classify-samples-from-dist.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_classify-samples-from-dist.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,118 @@ + + + - Run k-nearest-neighbors on a labeled distance matrix. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_classify-samples-ncv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_classify-samples-ncv.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,140 @@ + + + - Nested cross-validated supervised learning classifier. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_classify-samples.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_classify-samples.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,229 @@ + + + - Train and test a cross-validated supervised learning classifier. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_confusion-matrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_confusion-matrix.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,105 @@ + + + - Make a confusion matrix from sample classifier predictions. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_fit-classifier.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_fit-classifier.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,159 @@ + + + - Fit a supervised learning classifier. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_fit-regressor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_fit-regressor.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,161 @@ + + + - Fit a supervised learning regressor. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_heatmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_heatmap.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,360 @@ + + + - Generate heatmap of important features. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_maturity-index.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_maturity-index.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,203 @@ + + + - Microbial maturity index prediction. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_metatable.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_metatable.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,107 @@ + + + - Convert (and merge) positive numeric metadata (in)to feature table. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_predict-classification.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_predict-classification.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,57 @@ + + + - Use trained classifier to predict target values for new samples. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_predict-regression.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_predict-regression.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,57 @@ + + + - Use trained regressor to predict target values for new samples. + + qiime2 + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_regress-samples-ncv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_regress-samples-ncv.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,150 @@ + + + - Nested cross-validated supervised learning regressor. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_regress-samples.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_regress-samples.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,201 @@ + + + - Train and test a cross-validated supervised learning regressor. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_scatterplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_scatterplot.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,69 @@ + + + - Make 2D scatterplot and linear regression of regressor predictions. + + qiime2 + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_split-table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_split-table.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,113 @@ + + + - Split a feature table into training and testing sets. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_sample-classifier_summarize.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_sample-classifier_summarize.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,44 @@ + + + - Summarize parameter and feature extraction information for a trained estimator. + + qiime2 + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_taxa_barplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_taxa_barplot.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,70 @@ + + + - Visualize taxonomy with an interactive bar plot + + qiime2 + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_taxa_collapse.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_taxa_collapse.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,58 @@ + + + - Collapse features by their taxonomy at the specified level + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_taxa_filter-seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_taxa_filter-seqs.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,121 @@ + + + - Taxonomy-based feature sequence filter. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_taxa_filter-table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_taxa_filter-table.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,123 @@ + + + - Taxonomy-based feature table filter. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_tools_export.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_tools_export.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,30 @@ + + + - Export data from a QIIME 2 Artifact or Visualization. + + qiime2 + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_tools_export_collection.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_tools_export_collection.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,22 @@ + + + - Export data from a QIIME 2 Artifact or Visualization. + + qiime2 + + + + + + + + + + + + + + qiime_citation.xml + + + \ No newline at end of file diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_tools_export_paired_collection.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_tools_export_paired_collection.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,22 @@ + + + - Export data from a QIIME 2 Artifact or Visualization. + + qiime2 + + + + + + + + + + + + + + qiime_citation.xml + + + \ No newline at end of file diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_tools_import.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_tools_import.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,259 @@ + + + - Import data into a new QIIME 2 Artifact. + + qiime2 + + + $file_for_processing; + #else + #set $file_for_processing = "'input/" + $f.name + "'" + ln -s ${f} $file_for_processing; + #end if + #end for + #if 'SingleEndFastqManifestPhred' in str($sourceformat): + #set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt" + #set $m_file = open(str($cwd), 'w') + $m_file.write("sample-id,absolute-filepath,direction\n") + #for $f in $input_type.list_list: + $m_file.write(str($f.name).split("_")[0]+",$PWD/input/"+str($f.name)+".gz,forward\n") + #end for + $m_file.close() + #set $in_= str($cwd) + #end if + + +#elif $input_type.type == 'list_paired_collection': + + #set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt" + #set $m_file = open(str($cwd), 'w') + $m_file.write("sample-id,absolute-filepath,direction\n") + + #for $pair in $input_type.list_paired_collection: + #set $forward_is_fastq_file = $is_fastq(str($pair.forward)) + #set $reverse_is_fastq_file = $is_fastq(str($pair.reverse)) + + #if $forward_is_fastq_file: + gzip -c ${pair.forward} > input/${pair.name}_R1_001.fastq.gz; + $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n") + #else + ln -s ${pair.forward} input/${pair.name}_R1_001.fastq.gz; + $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n") + #end if + + #if $reverse_is_fastq_file: + gzip -c ${pair.reverse} > input/${pair.name}_R2_001.fastq.gz; + $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n") + #else + ln -s ${pair.reverse} input/${pair.name}_R2_001.fastq.gz; + $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n") + #end if + #end for + + + $m_file.close() + #if 'PairedEndFastqManifestPhred' in str($sourceformat): + #set $in_= str($cwd) + #elif 'Casava' in str($sourceformat): + #set $in_= 'input' + #end if + +#else + #set $res = $is_fastq(str($file)) + + #if $res + gzip -c ${file} > ${file.name}.gz; + #set $in_= $file.name + '.gz' + + #else + #set $in_= str($file) + #end if + + #if "MultiplexedSingleEndBarcodeInSequence" in str($semantic_type): + mv *_R1_* forward.fastq.gz; + #set $in_= 'forward.fastq.gz'; + #end if + +#end if + + +## rename files to predefined names for "MultiplexedPairedEndBarcodeInSequence" +#if "MultiplexedPairedEndBarcodeInSequence" in str($semantic_type): + mv input/*_R1_* input/forward.fastq.gz; + mv input/*_R2_* input/reverse.fastq.gz; +#end if + + +qiime tools import + +--type="$semantic_type" + +--input-path=$in_ + +--output-path=outputpath.qza + +#if str($sourceformat) != 'None': + #if '__ob__' in str($sourceformat): + #set $sourceformat_temp = str($sourceformat).replace('__ob__', '[') + #set $sourceformat_temp = str($sourceformat_temp).replace('__cb__', ']') + #set $sourceformat = $sourceformat_temp + #end if + --source-format="$sourceformat" +#end if +; +cp outputpath.qza $outputpath +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_vsearch_cluster-features-closed-reference.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_vsearch_cluster-features-closed-reference.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,104 @@ + + + - Closed-reference clustering of features. + + qiime2 + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_vsearch_cluster-features-de-novo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_vsearch_cluster-features-de-novo.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,72 @@ + + + - De novo clustering of features. + + qiime2 + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_vsearch_cluster-features-open-reference.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_vsearch_cluster-features-open-reference.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,105 @@ + + + - Open-reference clustering of features. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_vsearch_dereplicate-sequences.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_vsearch_dereplicate-sequences.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,61 @@ + + + - Dereplicate sequences. + + qiime2 + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_vsearch_join-pairs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_vsearch_join-pairs.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,139 @@ + + + - Join paired-end reads. + + qiime2 + + + + + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_vsearch_uchime-denovo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_vsearch_uchime-denovo.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,98 @@ + + + - De novo chimera filtering with vsearch. + + qiime2 + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 qiime2/qiime_vsearch_uchime-ref.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_vsearch_uchime-ref.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,109 @@ + + + - Reference-based chimera filtering with vsearch. + + qiime2 + + + + + + + + + + + + + + + + + + + + qiime_citation.xml + + + diff -r 000000000000 -r 370e0b6e9826 tool_data/ref_classifier.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data/ref_classifier.loc Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,5 @@ +# +# +#For each reference database, you need to download the qza file in qiime path +# + diff -r 000000000000 -r 370e0b6e9826 tool_data/ref_taxnonomy.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data/ref_taxnonomy.loc Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,5 @@ +# +# +#For each reference database, you need to download the qza file in qiime path +# + diff -r 000000000000 -r 370e0b6e9826 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,11 @@ + + + value, name, dbkey, path + +

+ + value, name, dbkey, path + +

+ +