# HG changeset patch
# User florianbegusch
# Date 1563342571 14400
# Node ID 149432539226aef82a0a5d9227c64864f1177152
# Parent 6851c25d84b740028bda77dd611bd0e66c10f112
Uploaded
diff -r 6851c25d84b7 -r 149432539226 qiime2/.idea/markdown-navigator/profiles_settings.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/.idea/markdown-navigator/profiles_settings.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,3 @@
+
+
+
\ No newline at end of file
diff -r 6851c25d84b7 -r 149432539226 qiime2/.idea/misc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/.idea/misc.xml Wed Jul 17 01:49:31 2019 -0400
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\ No newline at end of file
diff -r 6851c25d84b7 -r 149432539226 qiime2/.idea/modules.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/.idea/modules.xml Wed Jul 17 01:49:31 2019 -0400
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\ No newline at end of file
diff -r 6851c25d84b7 -r 149432539226 qiime2/.idea/qiime2.iml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/.idea/qiime2.iml Wed Jul 17 01:49:31 2019 -0400
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\ No newline at end of file
diff -r 6851c25d84b7 -r 149432539226 qiime2/.idea/vcs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/.idea/vcs.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,6 @@
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\ No newline at end of file
diff -r 6851c25d84b7 -r 149432539226 qiime2/.idea/workspace.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/.idea/workspace.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,518 @@
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+ 1.8
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+ 1.8
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\ No newline at end of file
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 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 6851c25d84b7 -r 149432539226 qiime2/qiime_alignment_mafft.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mafft.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,56 @@
+
+
+ - De novo multiple sequence alignment with MAFFT
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_alignment_mask.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mask.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,66 @@
+
+
+ - Positional conservation and gap filtering.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_citation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_citation.xml Wed Jul 17 01:49:31 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 = 2018,
+ 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 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,48 @@
+
+
+ - Add pseudocount to table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_composition_ancom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_composition_ancom.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,87 @@
+
+
+ - Apply ANCOM to identify features that differ in abundance.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ mean_difference
+ f_statistic
+
+
+
+ Selection is Optional
+ log
+ clr
+ sqrt
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,92 @@
+
+
+ - Demultiplex paired-end sequence data with barcodes in- sequence.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,76 @@
+
+
+ - Demultiplex single-end sequence data with barcodes in- sequence.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,190 @@
+
+
+ - Find and remove adapters in demultiplexed paired-end sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,151 @@
+
+
+ - Find and remove adapters in demultiplexed single-end sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,164 @@
+
+
+ - Denoise and dereplicate paired-end sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ consensus
+ pooled
+ none
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,149 @@
+
+
+ - Denoise and dereplicate single-end pyrosequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ consensus
+ pooled
+ none
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,140 @@
+
+
+ - Denoise and dereplicate single-end sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ consensus
+ pooled
+ none
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,128 @@
+
+
+ - Deblur sequences using a 16S positive filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,133 @@
+
+
+ - Deblur sequences using a user-specified positive filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,43 @@
+
+
+ - Visualize Deblur stats per sample.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,92 @@
+
+
+ - Demultiplex paired-end sequence data generated with the EMP protocol.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,93 @@
+
+
+ - Demultiplex sequence data generated with the EMP protocol.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,50 @@
+
+
+ - Subsample paired-end sequences without replacement.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,50 @@
+
+
+ - Subsample single-end sequences without replacement.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_demux_summarize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_summarize.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,55 @@
+
+
+ - Summarize counts per sample.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_diversity_adonis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_adonis.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,94 @@
+
+
+ - adonis PERMANOVA test for beta group significance
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,73 @@
+
+
+ - Alpha diversity correlation
+
+ qiime2
+
+
+
+
+
+ Selection is Optional
+ spearman
+ pearson
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,69 @@
+
+
+ - Alpha diversity comparisons
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,57 @@
+
+
+ - Alpha diversity (phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+ faith_pd
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,134 @@
+
+
+ - Alpha rarefaction curves
+
+ qiime2
+
+
+
+
+
+
+
+ Selection is Optional
+ dominance
+ ace
+ brillouin_d
+ margalef
+ menhinick
+ mcintosh_d
+ berger_parker_d
+ enspie
+ doubles
+ lladser_pe
+ observed_otus
+ faith_pd
+ simpson_e
+ robbins
+ shannon
+ pielou_e
+ singles
+ michaelis_menten_fit
+ heip_e
+ mcintosh_e
+ fisher_alpha
+ goods_coverage
+ chao1
+ gini_index
+ simpson
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_diversity_alpha.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,79 @@
+
+
+ - Alpha diversity
+
+ qiime2
+
+
+
+
+
+ menhinick
+ gini_index
+ chao1_ci
+ lladser_pe
+ observed_otus
+ lladser_ci
+ simpson_e
+ shannon
+ pielou_e
+ heip_e
+ mcintosh_e
+ osd
+ fisher_alpha
+ goods_coverage
+ strong
+ simpson
+ dominance
+ ace
+ brillouin_d
+ margalef
+ esty_ci
+ kempton_taylor_q
+ berger_parker_d
+ enspie
+ doubles
+ robbins
+ singles
+ mcintosh_d
+ chao1
+ michaelis_menten_fit
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,116 @@
+
+
+ - Beta diversity correlation
+
+ qiime2
+
+
+
+
+
+
+ Selection is Optional
+ spearman
+ pearson
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,95 @@
+
+
+ - Beta diversity group significance
+
+ qiime2
+
+
+
+
+
+
+ Selection is Optional
+ permanova
+ anosim
+ permdisp
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,112 @@
+
+
+ - Beta diversity (phylogenetic) - High Performance Computation
+
+ qiime2
+
+
+
+
+
+
+ generalized_unifrac
+ weighted_unifrac
+ weighted_normalized_unifrac
+ unweighted_unifrac
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,97 @@
+
+
+ - Beta diversity (phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+ generalized_unifrac
+ unweighted_unifrac
+ weighted_normalized_unifrac
+ weighted_unifrac
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,168 @@
+
+
+ - Beta diversity rarefaction
+
+ qiime2
+
+
+
+
+
+ kulsinski
+ euclidean
+ wminkowski
+ dice
+ correlation
+ hamming
+ canberra
+ canberra_adkins
+ rogerstanimoto
+ sqeuclidean
+ cosine
+ seuclidean
+ weighted_normalized_unifrac
+ sokalmichener
+ unweighted_unifrac
+ cityblock
+ generalized_unifrac
+ weighted_unifrac
+ braycurtis
+ jaccard
+ sokalsneath
+ aitchison
+ matching
+ chebyshev
+ russellrao
+ yule
+ mahalanobis
+
+
+ upgma
+ nj
+
+
+
+
+
+ Selection is Optional
+ spearman
+ pearson
+
+
+ Selection is Optional
+ BrBG
+ BrBG_r
+ PRGn
+ PRGn_r
+ PiYG
+ PiYG_r
+ PuOr
+ PuOr_r
+ RdBu
+ RdBu_r
+ RdGy
+ RdGy_r
+ RdYlBu
+ RdYlBu_r
+ RdYlGn
+ RdYlGn_r
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_diversity_beta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,85 @@
+
+
+ - Beta diversity
+
+ qiime2
+
+
+
+
+
+ kulsinski
+ wminkowski
+ correlation
+ hamming
+ canberra
+ canberra_adkins
+ sqeuclidean
+ sokalmichener
+ cityblock
+ braycurtis
+ matching
+ russellrao
+ cosine
+ yule
+ euclidean
+ rogerstanimoto
+ seuclidean
+ jaccard
+ sokalsneath
+ aitchison
+ chebyshev
+ dice
+ mahalanobis
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_diversity_bioenv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_bioenv.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,68 @@
+
+
+ - bioenv
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,167 @@
+
+
+ - Core diversity metrics (phylogenetic and non- phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,121 @@
+
+
+ - Core diversity metrics (non-phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,92 @@
+
+
+ - Filter samples from a distance matrix.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_diversity_mantel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_mantel.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,98 @@
+
+
+ - Apply the Mantel test to two distance matrices
+
+ qiime2
+
+
+
+
+
+
+ Selection is Optional
+ spearman
+ pearson
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,49 @@
+
+
+ - Principal Coordinate Analysis Biplot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_diversity_pcoa.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_pcoa.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,58 @@
+
+
+ - Principal Coordinate Analysis
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,58 @@
+
+
+ - Procrustes Analysis
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_emperor_biplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_emperor_biplot.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,89 @@
+
+
+ - Visualize and Interact with Principal Coordinates Analysis Biplot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_emperor_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_emperor_plot.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,83 @@
+
+
+ - Visualize and Interact with Principal Coordinates Analysis Plots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,88 @@
+
+
+ - Visualize and Interact with a procrustes plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,140 @@
+
+
+ - BLAST+ consensus taxonomy classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+ Public databases
+ Databases from your history
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ both
+ plus
+ minus
+
+
+
+
+
+
+
+
+ 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 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,135 @@
+
+
+ - VSEARCH consensus taxonomy classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+ Public databases
+ Databases from your history
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ both
+ plus
+
+
+
+
+
+
+
+ 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 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,81 @@
+
+
+ - Pre-fitted sklearn-based taxonomy classifier
+
+ qiime2
+
+
+
+
+
+
+
+ Selection is Optional
+ same
+ reverse-complement
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,91 @@
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,260 @@
+
+
+ - Train the naive_bayes classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+ Public databases
+ Databases from your history
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,86 @@
+
+
+ - Train an almost arbitrary scikit-learn classifier
+
+ qiime2
+
+
+
+
+
+
+
+ Public databases
+ Databases from your history
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,69 @@
+
+
+ - Identify core features in table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,121 @@
+
+
+ - Filter features from table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,120 @@
+
+
+ - Filter samples from table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,97 @@
+
+
+ - Filter features from sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,87 @@
+
+
+ - Group samples or features by a metadata column
+
+ qiime2
+
+
+
+
+
+ feature
+ sample
+
+
+
+ median-ceiling
+ mean-ceiling
+ sum
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,332 @@
+
+
+ - Generate a heatmap representation of a feature table
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ kulsinski
+ correlation
+ hamming
+ canberra
+ sqeuclidean
+ sokalmichener
+ cityblock
+ braycurtis
+ matching
+ russellrao
+ cosine
+ yule
+ minkowski
+ euclidean
+ rogerstanimoto
+ seuclidean
+ jaccard
+ sokalsneath
+ chebyshev
+ dice
+ mahalanobis
+
+
+ Selection is Optional
+ complete
+ centroid
+ weighted
+ single
+ ward
+ average
+ median
+
+
+ Selection is Optional
+ features
+ both
+ samples
+ none
+
+
+ Selection is Optional
+ bone
+ PRGn_r
+ Vega10_r
+ GnBu
+ hsv
+ binary_r
+ GnBu_r
+ icefire
+ winter
+ BuGn_r
+ plasma_r
+ Vega20_r
+ summer_r
+ cool_r
+ Spectral
+ gist_heat_r
+ Vega20b_r
+ mako_r
+ RdBu_r
+ cubehelix
+ tab20b_r
+ CMRmap
+ Greys
+ PuOr
+ cubehelix_r
+ Wistia
+ gnuplot2
+ bwr
+ gnuplot_r
+ viridis
+ gist_ncar_r
+ gist_ncar
+ plasma
+ PuRd
+ afmhot
+ icefire_r
+ tab20b
+ gist_yarg_r
+ hot
+ YlOrRd_r
+ Vega20c
+ Dark2_r
+ Set3
+ PuBu
+ magma
+ Pastel2
+ terrain
+ autumn_r
+ spectral
+ brg
+ Set3_r
+ coolwarm
+ Set2_r
+ Paired_r
+ tab20c_r
+ mako
+ gist_rainbow_r
+ RdBu
+ PuBu_r
+ jet_r
+ gist_earth_r
+ Greys_r
+ gray
+ winter_r
+ rocket
+ Set2
+ seismic_r
+ Pastel1
+ RdYlGn_r
+ copper
+ spring_r
+ BuGn
+ Greens
+ Blues
+ PiYG_r
+ YlGnBu
+ Paired
+ YlGn_r
+ RdPu_r
+ BrBG_r
+ bone_r
+ RdYlBu
+ gist_rainbow
+ bwr_r
+ inferno_r
+ inferno
+ gist_stern_r
+ gray_r
+ Purples
+ RdGy
+ hot_r
+ YlOrBr_r
+ nipy_spectral
+ nipy_spectral_r
+ ocean
+ Set1
+ Dark2
+ Oranges
+ Pastel1_r
+ Oranges_r
+ Pastel2_r
+ YlGn
+ Vega20b
+ PuRd_r
+ PuBuGn_r
+ afmhot_r
+ spring
+ tab20_r
+ PuBuGn
+ gist_yarg
+ PiYG
+ flag
+ rainbow_r
+ hsv_r
+ prism_r
+ ocean_r
+ magma_r
+ flag_r
+ Blues_r
+ gnuplot2_r
+ gist_gray
+ spectral_r
+ CMRmap_r
+ rainbow
+ gnuplot
+ vlag
+ Set1_r
+ Accent
+ coolwarm_r
+ brg_r
+ pink_r
+ YlOrBr
+ Vega20c_r
+ Wistia_r
+ RdGy_r
+ tab20
+ BrBG
+ rocket_r
+ OrRd_r
+ YlGnBu_r
+ viridis_r
+ copper_r
+ gist_heat
+ Vega10
+ PuOr_r
+ binary
+ pink
+ Reds
+ Purples_r
+ cool
+ prism
+ terrain_r
+ BuPu_r
+ Spectral_r
+ Greens_r
+ gist_gray_r
+ RdYlGn
+ tab20c
+ Reds_r
+ tab10
+ summer
+ gist_stern
+ tab10_r
+ YlOrRd
+ jet
+ Vega20
+ vlag_r
+ RdPu
+ OrRd
+ Accent_r
+ autumn
+ BuPu
+ RdYlBu_r
+ gist_earth
+ seismic
+ PRGn
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,56 @@
+
+
+ - Combine collections of feature sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,56 @@
+
+
+ - Combine collections of feature taxonomies
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,66 @@
+
+
+ - Combine multiple tables
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ error_on_overlapping_sample
+ error_on_overlapping_feature
+ sum
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,43 @@
+
+
+ - Convert to presence/absence
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,58 @@
+
+
+ - Rarefy table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,43 @@
+
+
+ - Convert to relative frequencies
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,57 @@
+
+
+ - Subsample table
+
+ qiime2
+
+
+
+
+
+
+ sample
+ feature
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,58 @@
+
+
+ - Summarize table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,44 @@
+
+
+ - View sequence associated with each feature
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,43 @@
+
+
+ - Transpose a feature table.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,77 @@
+
+
+ - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
+
+ qiime2
+
+
+
+
+
+
+
+
+ Public databases
+ Databases from your history
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,66 @@
+
+
+ - Filter fragments in tree from table.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,103 @@
+
+
+ - Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,55 @@
+
+
+ - Add pseudocount to table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 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 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,111 @@
+
+
+ - Balance Summary
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,55 @@
+
+
+ - Hierarchical clustering using feature correlation.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,187 @@
+
+
+ - Dendrogram heatmap.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ clr
+ log
+
+
+ Selection is Optional
+ viridis
+ inferno
+ plasma
+ magma
+ Blues
+ BuGn
+ BuPu
+ GnBu
+ Greens
+ Greys
+ Oranges
+ OrRd
+ PuBu
+ PuBuGn
+ PuRd
+ Purples
+ RdPu
+ Reds
+ YlGn
+ YlGnBu
+ YlOrBr
+ YlOrRd
+ afmhot
+ autumn
+ bone
+ cool
+ copper
+ gist_heat
+ gray
+ hot
+ pink
+ spring
+ summer
+ winter
+ BrBG
+ bwr
+ coolwarm
+ PiYG
+ PRGn
+ PuOr
+ RdBu
+ RdGy
+ RdYlBu
+ RdYlGn
+ Spectral
+ seismic
+ Accent
+ Dark2
+ Paired
+ Pastel1
+ Pastel2
+ Set1
+ Set2
+ Set3
+ Vega10
+ Vega20
+ Vega20b
+ Vega20c
+ gist_earth
+ terrain
+ ocean
+ gist_stern
+ brg
+ CMRmap
+ cubehelix
+ gnuplot
+ gnuplot2
+ gist_ncar
+ nipy_spectral
+ jet
+ rainbow
+ gist_rainbow
+ hsv
+ flag
+ prism
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,79 @@
+
+
+ - Hierarchical clustering using gradient information.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,59 @@
+
+
+ - Isometric Log-ratio Transform applied to a hierarchical clustering
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,65 @@
+
+
+ - Isometric Log-ratio Transform applied to a phylogenetic tree
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,56 @@
+
+
+ - Isometric Log-ratio Transform
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,78 @@
+
+
+ - Simplicial Linear mixed effects regression
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,80 @@
+
+
+ - Simplicial Ordinary Least Squares Regression
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_longitudinal_anova.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_anova.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,87 @@
+
+
+ - ANOVA test
+
+ qiime2
+
+
+
+
+
+ Selection is Optional
+ I
+ II
+ III
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,176 @@
+
+
+ - Feature volatility analysis
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestRegressor
+ ExtraTreesRegressor
+ GradientBoostingRegressor
+ AdaBoostRegressor
+ ElasticNet
+ Ridge
+ Lasso
+ KNeighborsRegressor
+ LinearSVR
+ SVR
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,116 @@
+
+
+ - Compute first differences or difference from baseline between sequential states
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ error
+ random
+ drop
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,109 @@
+
+
+ - Compute first distances or distance from baseline between sequential states
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ error
+ random
+ drop
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,166 @@
+
+
+ - Linear mixed effects modeling
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ Set1
+ Set2
+ Set3
+ Pastel1
+ Pastel2
+ Paired
+ Accent
+ Dark2
+ tab10
+ tab20
+ tab20b
+ tab20c
+ viridis
+ plasma
+ inferno
+ magma
+ terrain
+ rainbow
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,255 @@
+
+
+ - Microbial maturity index prediction.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestRegressor
+ ExtraTreesRegressor
+ GradientBoostingRegressor
+ AdaBoostRegressor
+ ElasticNet
+ Ridge
+ Lasso
+ KNeighborsRegressor
+ LinearSVR
+ SVR
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_longitudinal_nmit.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_nmit.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,92 @@
+
+
+ - Nonparametric microbial interdependence test
+
+ qiime2
+
+
+
+
+
+
+ Selection is Optional
+ kendall
+ pearson
+ spearman
+
+
+ Selection is Optional
+ fro
+ nuc
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,157 @@
+
+
+ - Paired difference testing and boxplots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ Set1
+ Set2
+ Set3
+ Pastel1
+ Pastel2
+ Paired
+ Accent
+ Dark2
+ tab10
+ tab20
+ tab20b
+ tab20c
+ viridis
+ plasma
+ inferno
+ magma
+ terrain
+ rainbow
+
+
+ Selection is Optional
+ error
+ random
+ drop
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,144 @@
+
+
+ - Paired pairwise distance testing and boxplots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ Set1
+ Set2
+ Set3
+ Pastel1
+ Pastel2
+ Paired
+ Accent
+ Dark2
+ tab10
+ tab20
+ tab20b
+ tab20c
+ viridis
+ plasma
+ inferno
+ magma
+ terrain
+ rainbow
+
+
+ Selection is Optional
+ error
+ random
+ drop
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,105 @@
+
+
+ - Plot longitudinal feature volatility and importances
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ linear
+ pow
+ sqrt
+ log
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_longitudinal_volatility.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_volatility.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,116 @@
+
+
+ - Generate interactive volatility plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ linear
+ pow
+ sqrt
+ log
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,62 @@
+
+
+ - Create a distance matrix from a numeric Metadata column
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_metadata_tabulate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_metadata_tabulate.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,64 @@
+
+
+ - Interactively explore Metadata in an HTML table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,96 @@
+
+
+ - Build a phylogenetic tree using fasttree and mafft alignment
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_phylogeny_fasttree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_fasttree.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,47 @@
+
+
+ - Construct a phylogenetic tree with FastTree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,48 @@
+
+
+ - Remove features from table if they're not present in tree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,503 @@
+
+
+ - Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ JC
+ JC+I
+ JC+G
+ JC+I+G
+ JC+R2
+ JC+R3
+ JC+R4
+ JC+R5
+ JC+R6
+ JC+R7
+ JC+R8
+ JC+R9
+ JC+R10
+ F81
+ F81+I
+ F81+G
+ F81+I+G
+ F81+R2
+ F81+R3
+ F81+R4
+ F81+R5
+ F81+R6
+ F81+R7
+ F81+R8
+ F81+R9
+ F81+R10
+ K80
+ K80+I
+ K80+G
+ K80+I+G
+ K80+R2
+ K80+R3
+ K80+R4
+ K80+R5
+ K80+R6
+ K80+R7
+ K80+R8
+ K80+R9
+ K80+R10
+ HKY
+ HKY+I
+ HKY+G
+ HKY+I+G
+ HKY+R2
+ HKY+R3
+ HKY+R4
+ HKY+R5
+ HKY+R6
+ HKY+R7
+ HKY+R8
+ HKY+R9
+ HKY+R10
+ TNe
+ TNe+I
+ TNe+G
+ TNe+I+G
+ TNe+R2
+ TNe+R3
+ TNe+R4
+ TNe+R5
+ TNe+R6
+ TNe+R7
+ TNe+R8
+ TNe+R9
+ TNe+R10
+ TN
+ TN+I
+ TN+G
+ TN+I+G
+ TN+R2
+ TN+R3
+ TN+R4
+ TN+R5
+ TN+R6
+ TN+R7
+ TN+R8
+ TN+R9
+ TN+R10
+ K81
+ K81+I
+ K81+G
+ K81+I+G
+ K81+R2
+ K81+R3
+ K81+R4
+ K81+R5
+ K81+R6
+ K81+R7
+ K81+R8
+ K81+R9
+ K81+R10
+ K81u
+ K81u+I
+ K81u+G
+ K81u+I+G
+ K81u+R2
+ K81u+R3
+ K81u+R4
+ K81u+R5
+ K81u+R6
+ K81u+R7
+ K81u+R8
+ K81u+R9
+ K81u+R10
+ TPM2
+ TPM2+I
+ TPM2+G
+ TPM2+I+G
+ TPM2+R2
+ TPM2+R3
+ TPM2+R4
+ TPM2+R5
+ TPM2+R6
+ TPM2+R7
+ TPM2+R8
+ TPM2+R9
+ TPM2+R10
+ TPM2u
+ TPM2u+I
+ TPM2u+G
+ TPM2u+I+G
+ TPM2u+R2
+ TPM2u+R3
+ TPM2u+R4
+ TPM2u+R5
+ TPM2u+R6
+ TPM2u+R7
+ TPM2u+R8
+ TPM2u+R9
+ TPM2u+R10
+ TPM3
+ TPM3+I
+ TPM3+G
+ TPM3+I+G
+ TPM3+R2
+ TPM3+R3
+ TPM3+R4
+ TPM3+R5
+ TPM3+R6
+ TPM3+R7
+ TPM3+R8
+ TPM3+R9
+ TPM3+R10
+ TPM3u
+ TPM3u+I
+ TPM3u+G
+ TPM3u+I+G
+ TPM3u+R2
+ TPM3u+R3
+ TPM3u+R4
+ TPM3u+R5
+ TPM3u+R6
+ TPM3u+R7
+ TPM3u+R8
+ TPM3u+R9
+ TPM3u+R10
+ TIMe
+ TIMe+I
+ TIMe+G
+ TIMe+I+G
+ TIMe+R2
+ TIMe+R3
+ TIMe+R4
+ TIMe+R5
+ TIMe+R6
+ TIMe+R7
+ TIMe+R8
+ TIMe+R9
+ TIMe+R10
+ TIM
+ TIM+I
+ TIM+G
+ TIM+I+G
+ TIM+R2
+ TIM+R3
+ TIM+R4
+ TIM+R5
+ TIM+R6
+ TIM+R7
+ TIM+R8
+ TIM+R9
+ TIM+R10
+ TIM2e
+ TIM2e+I
+ TIM2e+G
+ TIM2e+I+G
+ TIM2e+R2
+ TIM2e+R3
+ TIM2e+R4
+ TIM2e+R5
+ TIM2e+R6
+ TIM2e+R7
+ TIM2e+R8
+ TIM2e+R9
+ TIM2e+R10
+ TIM2
+ TIM2+I
+ TIM2+G
+ TIM2+I+G
+ TIM2+R2
+ TIM2+R3
+ TIM2+R4
+ TIM2+R5
+ TIM2+R6
+ TIM2+R7
+ TIM2+R8
+ TIM2+R9
+ TIM2+R10
+ TIM3e
+ TIM3e+I
+ TIM3e+G
+ TIM3e+I+G
+ TIM3e+R2
+ TIM3e+R3
+ TIM3e+R4
+ TIM3e+R5
+ TIM3e+R6
+ TIM3e+R7
+ TIM3e+R8
+ TIM3e+R9
+ TIM3e+R10
+ TIM3
+ TIM3+I
+ TIM3+G
+ TIM3+I+G
+ TIM3+R2
+ TIM3+R3
+ TIM3+R4
+ TIM3+R5
+ TIM3+R6
+ TIM3+R7
+ TIM3+R8
+ TIM3+R9
+ TIM3+R10
+ TVMe
+ TVMe+I
+ TVMe+G
+ TVMe+I+G
+ TVMe+R2
+ TVMe+R3
+ TVMe+R4
+ TVMe+R5
+ TVMe+R6
+ TVMe+R7
+ TVMe+R8
+ TVMe+R9
+ TVMe+R10
+ TVM
+ TVM+I
+ TVM+G
+ TVM+I+G
+ TVM+R2
+ TVM+R3
+ TVM+R4
+ TVM+R5
+ TVM+R6
+ TVM+R7
+ TVM+R8
+ TVM+R9
+ TVM+R10
+ SYM
+ SYM+I
+ SYM+G
+ SYM+I+G
+ SYM+R2
+ SYM+R3
+ SYM+R4
+ SYM+R5
+ SYM+R6
+ SYM+R7
+ SYM+R8
+ SYM+R9
+ SYM+R10
+ GTR
+ GTR+I
+ GTR+G
+ GTR+I+G
+ GTR+R2
+ GTR+R3
+ GTR+R4
+ GTR+R5
+ GTR+R6
+ GTR+R7
+ GTR+R8
+ GTR+R9
+ GTR+R10
+ MFP
+ TEST
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_phylogeny_iqtree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_iqtree.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,470 @@
+
+
+ - Construct a phylogenetic tree with IQ-TREE.
+
+ qiime2
+
+
+
+
+
+
+
+ Selection is Optional
+ JC
+ JC+I
+ JC+G
+ JC+I+G
+ JC+R2
+ JC+R3
+ JC+R4
+ JC+R5
+ JC+R6
+ JC+R7
+ JC+R8
+ JC+R9
+ JC+R10
+ F81
+ F81+I
+ F81+G
+ F81+I+G
+ F81+R2
+ F81+R3
+ F81+R4
+ F81+R5
+ F81+R6
+ F81+R7
+ F81+R8
+ F81+R9
+ F81+R10
+ K80
+ K80+I
+ K80+G
+ K80+I+G
+ K80+R2
+ K80+R3
+ K80+R4
+ K80+R5
+ K80+R6
+ K80+R7
+ K80+R8
+ K80+R9
+ K80+R10
+ HKY
+ HKY+I
+ HKY+G
+ HKY+I+G
+ HKY+R2
+ HKY+R3
+ HKY+R4
+ HKY+R5
+ HKY+R6
+ HKY+R7
+ HKY+R8
+ HKY+R9
+ HKY+R10
+ TNe
+ TNe+I
+ TNe+G
+ TNe+I+G
+ TNe+R2
+ TNe+R3
+ TNe+R4
+ TNe+R5
+ TNe+R6
+ TNe+R7
+ TNe+R8
+ TNe+R9
+ TNe+R10
+ TN
+ TN+I
+ TN+G
+ TN+I+G
+ TN+R2
+ TN+R3
+ TN+R4
+ TN+R5
+ TN+R6
+ TN+R7
+ TN+R8
+ TN+R9
+ TN+R10
+ K81
+ K81+I
+ K81+G
+ K81+I+G
+ K81+R2
+ K81+R3
+ K81+R4
+ K81+R5
+ K81+R6
+ K81+R7
+ K81+R8
+ K81+R9
+ K81+R10
+ K81u
+ K81u+I
+ K81u+G
+ K81u+I+G
+ K81u+R2
+ K81u+R3
+ K81u+R4
+ K81u+R5
+ K81u+R6
+ K81u+R7
+ K81u+R8
+ K81u+R9
+ K81u+R10
+ TPM2
+ TPM2+I
+ TPM2+G
+ TPM2+I+G
+ TPM2+R2
+ TPM2+R3
+ TPM2+R4
+ TPM2+R5
+ TPM2+R6
+ TPM2+R7
+ TPM2+R8
+ TPM2+R9
+ TPM2+R10
+ TPM2u
+ TPM2u+I
+ TPM2u+G
+ TPM2u+I+G
+ TPM2u+R2
+ TPM2u+R3
+ TPM2u+R4
+ TPM2u+R5
+ TPM2u+R6
+ TPM2u+R7
+ TPM2u+R8
+ TPM2u+R9
+ TPM2u+R10
+ TPM3
+ TPM3+I
+ TPM3+G
+ TPM3+I+G
+ TPM3+R2
+ TPM3+R3
+ TPM3+R4
+ TPM3+R5
+ TPM3+R6
+ TPM3+R7
+ TPM3+R8
+ TPM3+R9
+ TPM3+R10
+ TPM3u
+ TPM3u+I
+ TPM3u+G
+ TPM3u+I+G
+ TPM3u+R2
+ TPM3u+R3
+ TPM3u+R4
+ TPM3u+R5
+ TPM3u+R6
+ TPM3u+R7
+ TPM3u+R8
+ TPM3u+R9
+ TPM3u+R10
+ TIMe
+ TIMe+I
+ TIMe+G
+ TIMe+I+G
+ TIMe+R2
+ TIMe+R3
+ TIMe+R4
+ TIMe+R5
+ TIMe+R6
+ TIMe+R7
+ TIMe+R8
+ TIMe+R9
+ TIMe+R10
+ TIM
+ TIM+I
+ TIM+G
+ TIM+I+G
+ TIM+R2
+ TIM+R3
+ TIM+R4
+ TIM+R5
+ TIM+R6
+ TIM+R7
+ TIM+R8
+ TIM+R9
+ TIM+R10
+ TIM2e
+ TIM2e+I
+ TIM2e+G
+ TIM2e+I+G
+ TIM2e+R2
+ TIM2e+R3
+ TIM2e+R4
+ TIM2e+R5
+ TIM2e+R6
+ TIM2e+R7
+ TIM2e+R8
+ TIM2e+R9
+ TIM2e+R10
+ TIM2
+ TIM2+I
+ TIM2+G
+ TIM2+I+G
+ TIM2+R2
+ TIM2+R3
+ TIM2+R4
+ TIM2+R5
+ TIM2+R6
+ TIM2+R7
+ TIM2+R8
+ TIM2+R9
+ TIM2+R10
+ TIM3e
+ TIM3e+I
+ TIM3e+G
+ TIM3e+I+G
+ TIM3e+R2
+ TIM3e+R3
+ TIM3e+R4
+ TIM3e+R5
+ TIM3e+R6
+ TIM3e+R7
+ TIM3e+R8
+ TIM3e+R9
+ TIM3e+R10
+ TIM3
+ TIM3+I
+ TIM3+G
+ TIM3+I+G
+ TIM3+R2
+ TIM3+R3
+ TIM3+R4
+ TIM3+R5
+ TIM3+R6
+ TIM3+R7
+ TIM3+R8
+ TIM3+R9
+ TIM3+R10
+ TVMe
+ TVMe+I
+ TVMe+G
+ TVMe+I+G
+ TVMe+R2
+ TVMe+R3
+ TVMe+R4
+ TVMe+R5
+ TVMe+R6
+ TVMe+R7
+ TVMe+R8
+ TVMe+R9
+ TVMe+R10
+ TVM
+ TVM+I
+ TVM+G
+ TVM+I+G
+ TVM+R2
+ TVM+R3
+ TVM+R4
+ TVM+R5
+ TVM+R6
+ TVM+R7
+ TVM+R8
+ TVM+R9
+ TVM+R10
+ SYM
+ SYM+I
+ SYM+G
+ SYM+I+G
+ SYM+R2
+ SYM+R3
+ SYM+R4
+ SYM+R5
+ SYM+R6
+ SYM+R7
+ SYM+R8
+ SYM+R9
+ SYM+R10
+ GTR
+ GTR+I
+ GTR+G
+ GTR+I+G
+ GTR+R2
+ GTR+R3
+ GTR+R4
+ GTR+R5
+ GTR+R6
+ GTR+R7
+ GTR+R8
+ GTR+R9
+ GTR+R10
+ MFP
+ TEST
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,42 @@
+
+
+ - Midpoint root an unrooted phylogenetic tree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,103 @@
+
+
+ - Construct a phylogenetic tree with bootstrap supports using RAxML.
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ Standard
+ SSE3
+ AVX2
+
+
+ Selection is Optional
+ GTRGAMMA
+ GTRGAMMAI
+ GTRCAT
+ GTRCATI
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_phylogeny_raxml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_raxml.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,94 @@
+
+
+ - Construct a phylogenetic tree with RAxML.
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ Standard
+ SSE3
+ AVX2
+
+
+ Selection is Optional
+ GTRGAMMA
+ GTRGAMMAI
+ GTRCAT
+ GTRCATI
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,182 @@
+
+
+ - Evaluate expected vs. observed taxonomic composition of samples
+
+ qiime2
+
+
+
+
+
+
+
+ Selection is Optional
+ Set1
+ Set2
+ Set3
+ Pastel1
+ Pastel2
+ Paired
+ Accent
+ Dark2
+ tab10
+ tab20
+ tab20b
+ tab20c
+ viridis
+ plasma
+ inferno
+ magma
+ terrain
+ rainbow
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,57 @@
+
+
+ - Compare query (observed) vs. reference (expected) sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,122 @@
+
+
+ - Evaluate expected vs. observed taxonomic assignments
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ Set1
+ Set2
+ Set3
+ Pastel1
+ Pastel2
+ Paired
+ Accent
+ Dark2
+ tab10
+ tab20
+ tab20b
+ tab20c
+ viridis
+ plasma
+ inferno
+ magma
+ terrain
+ rainbow
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,103 @@
+
+
+ - Exclude sequences by alignment
+
+ qiime2
+
+
+
+
+
+
+ Selection is Optional
+ blast
+ vsearch
+ blastn-short
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,81 @@
+
+
+ - Quality filter based on joined sequence quality scores.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,81 @@
+
+
+ - Quality filter based on sequence quality scores.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,118 @@
+
+
+ - Run k-nearest-neighbors on a labeled distance matrix.
+
+ qiime2
+
+
+
+
+
+
+
+ Selection is Optional
+ YellowOrangeBrown
+ YellowOrangeRed
+ OrangeRed
+ PurpleRed
+ RedPurple
+ BluePurple
+ GreenBlue
+ PurpleBlue
+ YellowGreen
+ summer
+ copper
+ viridis
+ plasma
+ inferno
+ magma
+ sirocco
+ drifting
+ melancholy
+ enigma
+ eros
+ spectre
+ ambition
+ mysteriousstains
+ daydream
+ solano
+ navarro
+ dandelions
+ deepblue
+ verve
+ greyscale
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,140 @@
+
+
+ - Nested cross-validated supervised learning classifier.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestClassifier
+ ExtraTreesClassifier
+ GradientBoostingClassifier
+ AdaBoostClassifier
+ KNeighborsClassifier
+ LinearSVC
+ SVC
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,229 @@
+
+
+ - Train and test a cross-validated supervised learning classifier.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestClassifier
+ ExtraTreesClassifier
+ GradientBoostingClassifier
+ AdaBoostClassifier
+ KNeighborsClassifier
+ LinearSVC
+ SVC
+
+
+
+
+ Selection is Optional
+ YellowOrangeBrown
+ YellowOrangeRed
+ OrangeRed
+ PurpleRed
+ RedPurple
+ BluePurple
+ GreenBlue
+ PurpleBlue
+ YellowGreen
+ summer
+ copper
+ viridis
+ plasma
+ inferno
+ magma
+ sirocco
+ drifting
+ melancholy
+ enigma
+ eros
+ spectre
+ ambition
+ mysteriousstains
+ daydream
+ solano
+ navarro
+ dandelions
+ deepblue
+ verve
+ greyscale
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,105 @@
+
+
+ - Make a confusion matrix from sample classifier predictions.
+
+ qiime2
+
+
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+ Selection is Optional
+ YellowOrangeBrown
+ YellowOrangeRed
+ OrangeRed
+ PurpleRed
+ RedPurple
+ BluePurple
+ GreenBlue
+ PurpleBlue
+ YellowGreen
+ summer
+ copper
+ viridis
+ plasma
+ inferno
+ magma
+ sirocco
+ drifting
+ melancholy
+ enigma
+ eros
+ spectre
+ ambition
+ mysteriousstains
+ daydream
+ solano
+ navarro
+ dandelions
+ deepblue
+ verve
+ greyscale
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,159 @@
+
+
+ - Fit a supervised learning classifier.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestClassifier
+ ExtraTreesClassifier
+ GradientBoostingClassifier
+ AdaBoostClassifier
+ KNeighborsClassifier
+ LinearSVC
+ SVC
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,161 @@
+
+
+ - Fit a supervised learning regressor.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestRegressor
+ ExtraTreesRegressor
+ GradientBoostingRegressor
+ AdaBoostRegressor
+ ElasticNet
+ Ridge
+ Lasso
+ KNeighborsRegressor
+ LinearSVR
+ SVR
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,360 @@
+
+
+ - Generate heatmap of important features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ kulsinski
+ correlation
+ hamming
+ canberra
+ sqeuclidean
+ sokalmichener
+ cityblock
+ braycurtis
+ matching
+ russellrao
+ cosine
+ yule
+ minkowski
+ euclidean
+ rogerstanimoto
+ seuclidean
+ jaccard
+ sokalsneath
+ chebyshev
+ dice
+ mahalanobis
+
+
+ Selection is Optional
+ complete
+ centroid
+ weighted
+ single
+ ward
+ average
+ median
+
+
+ Selection is Optional
+ features
+ both
+ samples
+ none
+
+
+ Selection is Optional
+ bone
+ PRGn_r
+ Vega10_r
+ GnBu
+ hsv
+ binary_r
+ GnBu_r
+ icefire
+ winter
+ BuGn_r
+ plasma_r
+ Vega20_r
+ summer_r
+ cool_r
+ Spectral
+ gist_heat_r
+ Vega20b_r
+ mako_r
+ RdBu_r
+ cubehelix
+ tab20b_r
+ CMRmap
+ Greys
+ PuOr
+ cubehelix_r
+ Wistia
+ gnuplot2
+ bwr
+ gnuplot_r
+ viridis
+ gist_ncar_r
+ gist_ncar
+ plasma
+ PuRd
+ afmhot
+ icefire_r
+ tab20b
+ gist_yarg_r
+ hot
+ YlOrRd_r
+ Vega20c
+ Dark2_r
+ Set3
+ PuBu
+ magma
+ Pastel2
+ terrain
+ autumn_r
+ spectral
+ brg
+ Set3_r
+ coolwarm
+ Set2_r
+ Paired_r
+ tab20c_r
+ mako
+ gist_rainbow_r
+ RdBu
+ PuBu_r
+ jet_r
+ gist_earth_r
+ Greys_r
+ gray
+ winter_r
+ rocket
+ Set2
+ seismic_r
+ Pastel1
+ RdYlGn_r
+ copper
+ spring_r
+ BuGn
+ Greens
+ Blues
+ PiYG_r
+ YlGnBu
+ Paired
+ YlGn_r
+ RdPu_r
+ BrBG_r
+ bone_r
+ RdYlBu
+ gist_rainbow
+ bwr_r
+ inferno_r
+ inferno
+ gist_stern_r
+ gray_r
+ Purples
+ RdGy
+ hot_r
+ YlOrBr_r
+ nipy_spectral
+ nipy_spectral_r
+ ocean
+ Set1
+ Dark2
+ Oranges
+ Pastel1_r
+ Oranges_r
+ Pastel2_r
+ YlGn
+ Vega20b
+ PuRd_r
+ PuBuGn_r
+ afmhot_r
+ spring
+ tab20_r
+ PuBuGn
+ gist_yarg
+ PiYG
+ flag
+ rainbow_r
+ hsv_r
+ prism_r
+ ocean_r
+ magma_r
+ flag_r
+ Blues_r
+ gnuplot2_r
+ gist_gray
+ spectral_r
+ CMRmap_r
+ rainbow
+ gnuplot
+ vlag
+ Set1_r
+ Accent
+ coolwarm_r
+ brg_r
+ pink_r
+ YlOrBr
+ Vega20c_r
+ Wistia_r
+ RdGy_r
+ tab20
+ BrBG
+ rocket_r
+ OrRd_r
+ YlGnBu_r
+ viridis_r
+ copper_r
+ gist_heat
+ Vega10
+ PuOr_r
+ binary
+ pink
+ Reds
+ Purples_r
+ cool
+ prism
+ terrain_r
+ BuPu_r
+ Spectral_r
+ Greens_r
+ gist_gray_r
+ RdYlGn
+ tab20c
+ Reds_r
+ tab10
+ summer
+ gist_stern
+ tab10_r
+ YlOrRd
+ jet
+ Vega20
+ vlag_r
+ RdPu
+ OrRd
+ Accent_r
+ autumn
+ BuPu
+ RdYlBu_r
+ gist_earth
+ seismic
+ PRGn
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,203 @@
+
+
+ - Microbial maturity index prediction.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ Ridge
+ RandomForestRegressor
+ GradientBoostingRegressor
+ ExtraTreesRegressor
+ SVR
+ ElasticNet
+ Lasso
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,107 @@
+
+
+ - Convert (and merge) positive numeric metadata (in)to feature table.
+
+ qiime2
+
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+ Selection is Optional
+ drop_samples
+ drop_features
+ error
+ fill
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,57 @@
+
+
+ - Use trained classifier to predict target values for new samples.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,57 @@
+
+
+ - Use trained regressor to predict target values for new samples.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,150 @@
+
+
+ - Nested cross-validated supervised learning regressor.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestRegressor
+ ExtraTreesRegressor
+ GradientBoostingRegressor
+ AdaBoostRegressor
+ ElasticNet
+ Ridge
+ Lasso
+ KNeighborsRegressor
+ LinearSVR
+ SVR
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,201 @@
+
+
+ - Train and test a cross-validated supervised learning regressor.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ RandomForestRegressor
+ ExtraTreesRegressor
+ GradientBoostingRegressor
+ AdaBoostRegressor
+ ElasticNet
+ Ridge
+ Lasso
+ KNeighborsRegressor
+ LinearSVR
+ SVR
+
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,69 @@
+
+
+ - Make 2D scatterplot and linear regression of regressor predictions.
+
+ qiime2
+
+
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,113 @@
+
+
+ - Split a feature table into training and testing sets.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ error
+ ignore
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,44 @@
+
+
+ - Summarize parameter and feature extraction information for a trained estimator.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_taxa_barplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_barplot.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,70 @@
+
+
+ - Visualize taxonomy with an interactive bar plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_taxa_collapse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_collapse.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,58 @@
+
+
+ - Collapse features by their taxonomy at the specified level
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,121 @@
+
+
+ - Taxonomy-based feature sequence filter.
+
+ qiime2
+
+
+
+
+
+
+
+ Public databases
+ Databases from your history
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ exact
+ contains
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,123 @@
+
+
+ - Taxonomy-based feature table filter.
+
+ qiime2
+
+
+
+
+
+
+
+ Public databases
+ Databases from your history
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ exact
+ contains
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 qiime2/qiime_tools_export.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_export.xml Wed Jul 17 01:49:31 2019 -0400
@@ -0,0 +1,30 @@
+
+
+ - Export data from a QIIME 2 Artifact or Visualization.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 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 6851c25d84b7 -r 149432539226 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 01:49:31 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 6851c25d84b7 -r 149432539226 qiime2/qiime_tools_import.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_import.xml Wed Jul 17 01:49:31 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
+]]>
+
+
+
+
+ Input file
+ Multiple pairs - Combo mode (list:paired collection)
+ Input list
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ DeblurStats
+ DistanceMatrix
+ EMPPairedEndSequences
+ EMPSingleEndSequences
+ FeatureData[AlignedSequence]
+ FeatureData[PairedEndSequence]
+ FeatureData[Sequence]
+ FeatureData[Taxonomy]
+ FeatureTable[Balance]
+ FeatureTable[Composition]
+ FeatureTable[Frequency]
+ FeatureTable[PresenceAbsence]
+ FeatureTable[RelativeFrequency]
+ Hierarchy
+ MultiplexedPairedEndBarcodeInSequence
+ MultiplexedSingleEndBarcodeInSequence
+ PCoAResults
+ Phylogeny[Rooted]
+ Phylogeny[Unrooted]
+ QualityFilterStats
+ RawSequences
+ SampleData[AlphaDiversity]
+ SampleData[BooleanSeries]
+ SampleData[DADA2Stats]
+ SampleData[FirstDifferences]
+ SampleData[JoinedSequencesWithQuality]
+ SampleData[PairedEndSequencesWithQuality]
+ SampleData[SequencesWithQuality]
+ SampleData[Sequences]
+ TaxonomicClassifier
+ UchimeStats
+
+
+
+ AlignedDNAFASTAFormat
+ AlignedDNASequencesDirectoryFormat
+ AlphaDiversityDirectoryFormat
+ AlphaDiversityFormat
+ BIOMV100DirFmt
+ BIOMV100Format
+ BIOMV210DirFmt
+ BIOMV210Format
+ BooleanSeriesDirectoryFormat
+ BooleanSeriesFormat
+ CasavaOneEightLanelessPerSampleDirFmt
+ CasavaOneEightSingleLanePerSampleDirFmt
+ DADA2StatsDirFmt
+ DADA2StatsFormat
+ DNAFASTAFormat
+ DNASequencesDirectoryFormat
+ DeblurStatsDirFmt
+ DeblurStatsFmt
+ DistanceMatrixDirectoryFormat
+ EMPPairedEndCasavaDirFmt
+ EMPPairedEndDirFmt
+ EMPSingleEndCasavaDirFmt
+ EMPSingleEndDirFmt
+ FastqGzFormat
+ FirstDifferencesDirectoryFormat
+ FirstDifferencesFormat
+ HeaderlessTSVTaxonomyDirectoryFormat
+ HeaderlessTSVTaxonomyFormat
+ LSMatFormat
+ MultiplexedPairedEndBarcodeInSequenceDirFmt
+ MultiplexedSingleEndBarcodeInSequenceDirFmt
+ NewickDirectoryFormat
+ NewickFormat
+ OrdinationDirectoryFormat
+ OrdinationFormat
+ PairedDNASequencesDirectoryFormat
+ PairedEndFastqManifestPhred33
+ PairedEndFastqManifestPhred64
+ QIIME1DemuxDirFmt
+ QIIME1DemuxFormat
+ QualityFilterStatsDirFmt
+ QualityFilterStatsFmt
+ SingleEndFastqManifestPhred33
+ SingleEndFastqManifestPhred64
+ SingleLanePerSamplePairedEndFastqDirFmt
+ SingleLanePerSampleSingleEndFastqDirFmt
+ TSVTaxonomyDirectoryFormat
+ TSVTaxonomyFormat
+ TaxonomicClassiferTemporaryPickleDirFmt
+ UchimeStatsDirFmt
+ UchimeStatsFmt
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,104 @@
+
+
+ - Closed-reference clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+ Selection is Optional
+ plus
+ both
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,72 @@
+
+
+ - De novo clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,105 @@
+
+
+ - Open-reference clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+ Selection is Optional
+ plus
+ both
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,61 @@
+
+
+ - Dereplicate sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,139 @@
+
+
+ - Join paired-end reads.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,98 @@
+
+
+ - De novo chimera filtering with vsearch.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 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 01:49:31 2019 -0400
@@ -0,0 +1,109 @@
+
+
+ - Reference-based chimera filtering with vsearch.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 6851c25d84b7 -r 149432539226 tool_data/ref_classifier.loc
--- a/tool_data/ref_classifier.loc Wed Jul 17 01:40:44 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#
-#
-#For each reference database, you need to download the qza file in qiime path
-#
-
diff -r 6851c25d84b7 -r 149432539226 tool_data/ref_taxnonomy.loc
--- a/tool_data/ref_taxnonomy.loc Wed Jul 17 01:40:44 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#
-#
-#For each reference database, you need to download the qza file in qiime path
-#
-
diff -r 6851c25d84b7 -r 149432539226 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Wed Jul 17 01:40:44 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-
-
- value, name, dbkey, path
-
-
-
- value, name, dbkey, path
-
-
-
-