# HG changeset patch
# User florianbegusch
# Date 1599225169 0
# Node ID 3ba9833030c1ccde9c0ed480303896614326da98
# Parent c28331a63dfdb339a57ac3a884295db399b6ba80
Uploaded
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,34 @@
+
+
+ - Merge features and taxonomy into a single biom file.
+
+ qiime2
+
+
+mkdir out;
+
+qiime tools export --input-path $taxonomy_qza --output-path out;
+qiime tools export --input-path $biom_qza --output-path out;
+
+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 c28331a63dfd -r 3ba9833030c1 qiime2/qiime_alignment_mafft-add.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mafft-add.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,79 @@
+
+
+ Add sequences to multiple sequence alignment with MAFFT.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_alignment_mafft.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mafft.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,74 @@
+
+
+ De novo multiple sequence alignment with MAFFT
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_alignment_mask.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mask.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,74 @@
+
+
+ Positional conservation and gap filtering.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_citation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_citation.xml Fri Sep 04 13:12:49 2020 +0000
@@ -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 c28331a63dfd -r 3ba9833030c1 qiime2/qiime_composition_add-pseudocount.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_composition_add-pseudocount.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,59 @@
+
+
+ Add pseudocount to table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_composition_ancom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_composition_ancom.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,126 @@
+
+
+ Apply ANCOM to identify features that differ in abundance.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_cutadapt_demux-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_demux-paired.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,170 @@
+
+
+ Demultiplex paired-end sequence data with barcodes in- sequence.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_cutadapt_demux-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_demux-single.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,120 @@
+
+
+ Demultiplex single-end sequence data with barcodes in- sequence.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_cutadapt_trim-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_trim-paired.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,219 @@
+
+
+ Find and remove adapters in demultiplexed paired-end sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_cutadapt_trim-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_trim-single.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,167 @@
+
+
+ Find and remove adapters in demultiplexed single-end sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_dada2_denoise-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_dada2_denoise-paired.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,187 @@
+
+
+ Denoise and dereplicate paired-end sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_dada2_denoise-pyro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_dada2_denoise-pyro.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,166 @@
+
+
+ Denoise and dereplicate single-end pyrosequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_dada2_denoise-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_dada2_denoise-single.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,159 @@
+
+
+ Denoise and dereplicate single-end sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_deblur_denoise-16S.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_deblur_denoise-16S.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,126 @@
+
+
+ Deblur sequences using a 16S positive filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_deblur_denoise-other.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_deblur_denoise-other.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,132 @@
+
+
+ Deblur sequences using a user-specified positive filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_deblur_visualize-stats.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_deblur_visualize-stats.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,59 @@
+
+
+ Visualize Deblur stats per sample.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_demux_emp-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_emp-paired.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,125 @@
+
+
+ Demultiplex paired-end sequence data generated with the EMP protocol.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_demux_emp-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_emp-single.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,125 @@
+
+
+ Demultiplex sequence data generated with the EMP protocol.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_demux_filter-samples.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_filter-samples.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,113 @@
+
+
+ Filter samples out of demultiplexed data.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_demux_subsample-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_subsample-paired.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,63 @@
+
+
+ Subsample paired-end sequences without replacement.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_demux_subsample-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_subsample-single.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,63 @@
+
+
+ Subsample single-end sequences without replacement.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_demux_summarize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_summarize.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,79 @@
+
+
+ Summarize counts per sample.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_alpha-passthrough.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_alpha-passthrough.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,88 @@
+
+
+ Alpha Passthrough (non-phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_beta-passthrough.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_beta-passthrough.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,103 @@
+
+
+ Beta Passthrough (non-phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_beta-phylogenetic-passthrough.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_beta-phylogenetic-passthrough.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,117 @@
+
+
+ Beta Phylogenetic Passthrough
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_bray-curtis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_bray-curtis.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,73 @@
+
+
+ Bray-Curtis Dissimilarity
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_faith-pd.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_faith-pd.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,66 @@
+
+
+ Faith\'s Phylogenetic Diversity
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_jaccard.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_jaccard.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,71 @@
+
+
+ Jaccard Distance
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_observed-features.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_observed-features.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,58 @@
+
+
+ Observed Features
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_pielou-evenness.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_pielou-evenness.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,63 @@
+
+
+ Pielou\'s Evenness
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_shannon-entropy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_shannon-entropy.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,63 @@
+
+
+ Shannon\'s Entropy
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_unweighted-unifrac.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_unweighted-unifrac.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,86 @@
+
+
+ Unweighted Unifrac
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity-lib_weighted-unifrac.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_weighted-unifrac.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,86 @@
+
+
+ Weighted Unifrac
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_adonis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_adonis.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,108 @@
+
+
+ adonis PERMANOVA test for beta group significance
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_alpha-correlation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-correlation.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,95 @@
+
+
+ Alpha diversity correlation
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,80 @@
+
+
+ Alpha diversity comparisons
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_alpha-phylogenetic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-phylogenetic.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,71 @@
+
+
+ Alpha diversity (phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_alpha-rarefaction.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-rarefaction.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,141 @@
+
+
+ Alpha rarefaction curves
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_alpha.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,91 @@
+
+
+ Alpha diversity
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_beta-correlation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta-correlation.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,160 @@
+
+
+ Beta diversity correlation
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,132 @@
+
+
+ Beta diversity group significance
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_beta-phylogenetic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta-phylogenetic.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,117 @@
+
+
+ Beta diversity (phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_beta-rarefaction.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta-rarefaction.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,181 @@
+
+
+ Beta diversity rarefaction
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_beta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,105 @@
+
+
+ Beta diversity
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_bioenv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_bioenv.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,84 @@
+
+
+ bioenv
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,205 @@
+
+
+ Core diversity metrics (phylogenetic and non- phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_core-metrics.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_core-metrics.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,156 @@
+
+
+ Core diversity metrics (non-phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,114 @@
+
+
+ Filter samples from a distance matrix.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_mantel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_mantel.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,111 @@
+
+
+ Apply the Mantel test to two distance matrices
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_pcoa-biplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_pcoa-biplot.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,62 @@
+
+
+ Principal Coordinate Analysis Biplot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_pcoa.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_pcoa.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,69 @@
+
+
+ Principal Coordinate Analysis
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_diversity_procrustes-analysis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_procrustes-analysis.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,68 @@
+
+
+ Procrustes Analysis
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_emperor_biplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_emperor_biplot.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,117 @@
+
+
+ Visualize and Interact with Principal Coordinates Analysis Biplot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_emperor_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_emperor_plot.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,99 @@
+
+
+ Visualize and Interact with Principal Coordinates Analysis Plots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_emperor_procrustes-plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_emperor_procrustes-plot.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,110 @@
+
+
+ Visualize and Interact with a procrustes plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,119 @@
+
+
+ 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
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,197 @@
+
+
+ VSEARCH-based consensus taxonomy classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ perc_identity similarity. Note that if strand=both, maxaccepts
+ will keep N hits for each direction (if searches in the opposite
+ direction yield results that exceed the minimum perc_identity). In
+ those cases use maxhits to control the total number of hits returned.
+ This option works in pair with maxrejects. The search process sorts
+ target sequences by decreasing number of k-mers they have in common
+ with the query sequence, using that information as a proxy for sequence
+ similarity. After pairwise alignments, if the first target sequence
+ passes the acceptation criteria, it is accepted as best hit and the
+ search process stops for that query. If maxaccepts is set to a higher
+ value, more hits are accepted. If maxaccepts and maxrejects are both
+ set to "all", the complete database is searched.
+perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ Reject match if percent identity to query is lower.
+query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ Reject match if query alignment coverage per high-scoring pair is
+ lower.
+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.
+unassignable_label : Str, optional
+search_exact : Bool, optional
+ Search for exact full-length matches to the query sequences. Only 100%
+ exact matches are reported and this command is much faster than the
+ default. If True, the perc_identity and query_cov settings are ignored.
+ Note: query and reference reads must be trimmed to the exact same DNA
+ locus (e.g., primer site) because only exact matches will be reported.
+top_hits_only : Bool, optional
+ Only the top hits between the query and reference sequence sets are
+ reported. For each query, the top hit is the one presenting the highest
+ percentage of identity. Multiple equally scored top hits will be used
+ for consensus taxonomic assignment if maxaccepts is greater than 1.
+maxhits : Int % Range(1, None) | Str % Choices('all'), optional
+ Maximum number of hits to show once the search is terminated.
+maxrejects : Int % Range(1, None) | Str % Choices('all'), optional
+ Maximum number of non-matching target sequences to consider before
+ stopping the search. This option works in pair with maxaccepts (see
+ maxaccepts description for details).
+output_no_hits : Bool, optional
+ Report both matching and non-matching queries. WARNING: always use the
+ default setting for this option unless if you know what you are doing!
+ If you set this option to False, your sequences and feature table will
+ need to be filtered to exclude unclassified sequences, otherwise you
+ may run into errors downstream from missing feature IDs.
+weak_id : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ Show hits with percentage of identity of at least N, without
+ terminating the search. A normal search stops as soon as enough hits
+ are found (as defined by maxaccepts, maxrejects, and perc_identity). As
+ weak_id reports weak hits that are not deduced from maxaccepts, high
+ perc_identity values can be used, hence preserving both speed and
+ sensitivity. Logically, weak_id must be smaller than the value
+ indicated by perc_identity, otherwise this option will be ignored.
+threads : Int % Range(1, None), optional
+ Number of threads to use for job parallelization.
+
+Returns
+-------
+classification : FeatureData[Taxonomy]
+ The resulting taxonomy classifications.
+ ]]>
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-classifier_classify-hybrid-vsearch-sklearn.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-classifier_classify-hybrid-vsearch-sklearn.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,214 @@
+
+
+ ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ perc_identity similarity. Note that if strand=both, maxaccepts
+ will keep N hits for each direction (if searches in the opposite
+ direction yield results that exceed the minimum perc_identity). In
+ those cases use maxhits to control the total number of hits returned.
+ This option works in pair with maxrejects. The search process sorts
+ target sequences by decreasing number of k-mers they have in common
+ with the query sequence, using that information as a proxy for sequence
+ similarity. After pairwise alignments, if the first target sequence
+ passes the acceptation criteria, it is accepted as best hit and the
+ search process stops for that query. If maxaccepts is set to a higher
+ value, more hits are accepted. If maxaccepts and maxrejects are both
+ set to "all", the complete database is searched.
+perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ Percent sequence similarity to use for PREFILTER. Reject match if
+ percent identity to query is lower. Set to a lower value to perform a
+ rough pre-filter. This parameter is ignored if `prefilter` is disabled.
+query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ Query coverage threshold to use for PREFILTER. Reject match if query
+ alignment coverage per high-scoring pair is lower. Set to a lower value
+ to perform a rough pre-filter. This parameter is ignored if `prefilter`
+ is disabled.
+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.
+maxhits : Int % Range(1, None) | Str % Choices('all'), optional
+maxrejects : Int % Range(1, None) | Str % Choices('all'), optional
+reads_per_batch : Int % Range(0, None), optional
+ Number of reads to process in each batch for sklearn classification. If
+ "auto", this parameter is autoscaled to min(number of query sequences /
+ threads, 20000).
+confidence : Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable'), optional
+ Confidence threshold for limiting taxonomic depth. Set to "disable" to
+ disable confidence calculation, or 0 to calculate confidence but not
+ apply it to limit the taxonomic depth of the assignments.
+read_orientation : Str % Choices('same', 'reverse-complement', 'auto'), optional
+ Direction of reads with respect to reference sequences in pre-trained
+ sklearn classifier. same will cause reads to be classified unchanged;
+ reverse-complement will cause reads to be reversed and complemented
+ prior to classification. "auto" will autodetect orientation based on
+ the confidence estimates for the first 100 reads.
+threads : Int % Range(1, None), optional
+ Number of threads to use for job parallelization.
+prefilter : Bool, optional
+ Toggle positive filter of query sequences on or off.
+sample_size : Int % Range(1, None), optional
+ Randomly extract the given number of sequences from the reference
+ database to use for prefiltering. This parameter is ignored if
+ `prefilter` is disabled.
+randseed : Int % Range(0, None), optional
+ Use integer as a seed for the pseudo-random generator used during
+ prefiltering. A given seed always produces the same output, which is
+ useful for replicability. Set to 0 to use a pseudo-random seed. This
+ parameter is ignored if `prefilter` is disabled.
+
+Returns
+-------
+classification : FeatureData[Taxonomy]
+ The resulting taxonomy classifications.
+ ]]>
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,101 @@
+
+
+ Pre-fitted sklearn-based taxonomy classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,130 @@
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,208 @@
+
+
+ Train the naive_bayes classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,66 @@
+
+
+ Train an almost arbitrary scikit-learn classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,82 @@
+
+
+ Identify core features in table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,138 @@
+
+
+ Filter features from table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,137 @@
+
+
+ Filter samples from table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,130 @@
+
+
+ Filter features from sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_group.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_group.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,119 @@
+
+
+ Group samples or features by a metadata column
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_heatmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_heatmap.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,410 @@
+
+
+ Generate a heatmap representation of a feature table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,67 @@
+
+
+ Combine collections of feature sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,68 @@
+
+
+ Combine collections of feature taxonomies
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_merge.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_merge.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,76 @@
+
+
+ Combine multiple tables
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,59 @@
+
+
+ Convert to presence/absence
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_rarefy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_rarefy.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,71 @@
+
+
+ Rarefy table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,55 @@
+
+
+ Convert to relative frequencies
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_rename-ids.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_rename-ids.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,118 @@
+
+
+ Renames sample or feature ids in a table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_subsample.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_subsample.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,71 @@
+
+
+ Subsample table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_summarize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_summarize.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,74 @@
+
+
+ Summarize table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,76 @@
+
+
+ View sequence associated with each feature
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_feature-table_transpose.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_transpose.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,55 @@
+
+
+ Transpose a feature table.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,69 @@
+
+
+ Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,79 @@
+
+
+ Filter fragments in tree from table.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_fragment-insertion_sepp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_fragment-insertion_sepp.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,91 @@
+
+
+ Insert fragment sequences using SEPP into reference phylogenies.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_gneiss_assign-ids.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_assign-ids.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,67 @@
+
+
+ Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_gneiss_correlation-clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_correlation-clustering.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,65 @@
+
+
+ Hierarchical clustering using feature correlation.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_gneiss_dendrogram-heatmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_dendrogram-heatmap.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,222 @@
+
+
+ Dendrogram heatmap.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_gneiss_gradient-clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_gradient-clustering.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,108 @@
+
+
+ Hierarchical clustering using gradient information.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_gneiss_ilr-hierarchical.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_ilr-hierarchical.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,70 @@
+
+
+ Isometric Log-ratio Transform applied to a hierarchical clustering
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_gneiss_ilr-phylogenetic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_ilr-phylogenetic.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,76 @@
+
+
+ Isometric Log-ratio Transform applied to a phylogenetic tree
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_anova.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_anova.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,100 @@
+
+
+ ANOVA test
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_feature-volatility.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_feature-volatility.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,242 @@
+
+
+ Feature volatility analysis
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_first-differences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_first-differences.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,169 @@
+
+
+ Compute first differences or difference from baseline between sequential states
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_first-distances.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_first-distances.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,161 @@
+
+
+ Compute first distances or distance from baseline between sequential states
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,240 @@
+
+
+ Linear mixed effects modeling
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_maturity-index.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_maturity-index.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,299 @@
+
+
+ Microbial maturity index prediction.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_nmit.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_nmit.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,122 @@
+
+
+ Nonparametric microbial interdependence test
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_pairwise-differences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_pairwise-differences.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,237 @@
+
+
+ Paired difference testing and boxplots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_pairwise-distances.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_pairwise-distances.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,234 @@
+
+
+ Paired pairwise distance testing and boxplots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,235 @@
+
+
+ Plot longitudinal feature volatility and importances
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_longitudinal_volatility.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_volatility.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,208 @@
+
+
+ Generate interactive volatility plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,118 @@
+
+
+ Build a phylogenetic tree using fasttree and mafft alignment
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_align-to-tree-mafft-iqtree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_align-to-tree-mafft-iqtree.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,447 @@
+
+
+ Build a phylogenetic tree using iqtree and mafft alignment.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_align-to-tree-mafft-raxml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_align-to-tree-mafft-raxml.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,155 @@
+
+
+ Build a phylogenetic tree using raxml and mafft alignment.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_fasttree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_fasttree.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,69 @@
+
+
+ Construct a phylogenetic tree with FastTree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_filter-table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_filter-table.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,61 @@
+
+
+ Remove features from table if they\'re not present in tree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,513 @@
+
+
+ Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_iqtree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_iqtree.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,484 @@
+
+
+ Construct a phylogenetic tree with IQ-TREE.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_midpoint-root.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_midpoint-root.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,54 @@
+
+
+ Midpoint root an unrooted phylogenetic tree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,109 @@
+
+
+ Construct a phylogenetic tree with bootstrap supports using RAxML.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_raxml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_raxml.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,101 @@
+
+
+ Construct a phylogenetic tree with RAxML.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_phylogeny_robinson-foulds.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_robinson-foulds.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,78 @@
+
+
+ Calculate Robinson-Foulds distance between phylogenetic trees.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_quality-control_bowtie2-build.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_quality-control_bowtie2-build.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,58 @@
+
+
+ Build bowtie2 index from reference sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,214 @@
+
+
+ Evaluate expected vs. observed taxonomic composition of samples
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,80 @@
+
+
+ Compare query (observed) vs. reference (expected) sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,151 @@
+
+
+ Evaluate expected vs. observed taxonomic assignments
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,119 @@
+
+
+ Exclude sequences by alignment
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_quality-control_filter-reads.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_quality-control_filter-reads.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,110 @@
+
+
+ Filter demultiplexed sequences by alignment to reference database.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,85 @@
+
+
+ Quality filter based on sequence quality scores.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,151 @@
+
+
+ Run k-nearest-neighbors on a labeled distance matrix.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,170 @@
+
+
+ Nested cross-validated supervised learning classifier.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,260 @@
+
+
+ Train and test a cross-validated supervised learning classifier.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,178 @@
+
+
+ Make a confusion matrix from sample classifier predictions.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,179 @@
+
+
+ Fit a supervised learning classifier.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,181 @@
+
+
+ Fit a supervised learning regressor.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_sample-classifier_heatmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_sample-classifier_heatmap.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,440 @@
+
+
+ Generate heatmap of important features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_sample-classifier_metatable.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_sample-classifier_metatable.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,120 @@
+
+
+ Convert (and merge) positive numeric metadata (in)to feature table.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,73 @@
+
+
+ Use trained classifier to predict target values for new samples.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,68 @@
+
+
+ Use trained regressor to predict target values for new samples.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,176 @@
+
+
+ Nested cross-validated supervised learning regressor.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,227 @@
+
+
+ Train and test a cross-validated supervised learning regressor.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_sample-classifier_scatterplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_sample-classifier_scatterplot.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,107 @@
+
+
+ Make 2D scatterplot and linear regression of regressor predictions.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,136 @@
+
+
+ Split a feature table into training and testing sets.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_sample-classifier_summarize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_sample-classifier_summarize.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,61 @@
+
+
+ Summarize parameter and feature extraction information for a trained estimator.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_taxa_barplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_barplot.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,90 @@
+
+
+ Visualize taxonomy with an interactive bar plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_taxa_collapse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_collapse.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,72 @@
+
+
+ Collapse features by their taxonomy at the specified level
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_taxa_filter-seqs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_filter-seqs.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,107 @@
+
+
+ Taxonomy-based feature sequence filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_taxa_filter-table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_filter-table.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,109 @@
+
+
+ Taxonomy-based feature table filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_tools_export.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_export.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,30 @@
+
+
+ - Export data from a QIIME 2 Artifact or Visualization.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_tools_export_collection.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_export_collection.xml Fri Sep 04 13:12:49 2020 +0000
@@ -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 c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -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 c28331a63dfd -r 3ba9833030c1 qiime2/qiime_tools_import.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_import.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,291 @@
+
+
+ - Import data into a new QIIME 2 Artifact.
+
+ qiime2
+
+
+ $file_for_processing;
+ ##echo $is_fastq_file;
+ #else
+ #set $file_for_processing = "'input/" + $f.name + "'"
+ ln -s ${f} $file_for_processing;
+ ##echo $is_fastq_file;
+ #end if
+ #end for
+ #if 'SingleEndFastqManifestPhred' in str($inputformat):
+ #set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt"
+ #set $tt = str("sample-id,absolute-filepath,direction")
+ echo $tt >> $cwf;
+ #for $f in $input_type.list_list:
+ #set $tt = str($f.name).split("_")[0]+",$PWD/input/"+str($f.name).split(".")[0]+".fastq.gz,forward\n"
+ echo $tt >> $cwf;
+ #end for
+
+ #set $in_= str($cwf)
+ #end if
+
+
+#elif $input_type.type == 'list_paired_collection':
+
+ #set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt"
+ #set $tt = str("sample-id,absolute-filepath,direction")
+ echo $tt >> $cwf;
+
+ #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;
+ #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n"
+ echo $tt >> $cwf;
+ #else
+ ln -s ${pair.forward} input/${pair.name}_R1_001.fastq.gz;
+ #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n"
+ echo $tt >> $cwf;
+ #end if
+
+ #if $reverse_is_fastq_file:
+ gzip -c ${pair.reverse} > input/${pair.name}_R2_001.fastq.gz;
+ #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n"
+ echo $tt >> $cwf;
+ #else
+ ln -s ${pair.reverse} input/${pair.name}_R2_001.fastq.gz;
+ #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n"
+ echo $tt >> $cwf;
+ #end if
+ #end for
+
+
+
+ #if 'PairedEndFastqManifestPhred' in str($inputformat) or 'SingleEndFastqManifestPhred33V2' in str($inputformat) or 'SingleEndFastqManifestPhred33' in str($inputformat):
+
+ #set $in_= str($cwf)
+
+ #elif 'Casava' in str($inputformat):
+ #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
+
+--input-path=$in_
+
+#if str($inputformat) != 'None':
+ #if '__ob__' in str($inputformat):
+ #set $inputformat_temp = str($inputformat).replace('__ob__', '[')
+ #set $inputformat_temp = str($inputformat_temp).replace('__cb__', ']')
+ #set $inputformat = $inputformat_temp
+ #end if
+ --input-format="$inputformat"
+#end if
+
+--type="$semantic_type"
+
+--output-path=outputpath.qza
+
+;
+cp outputpath.qza $outputpath
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,110 @@
+
+
+ Closed-reference clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,86 @@
+
+
+ De novo clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 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 Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,119 @@
+
+
+ Open-reference clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_vsearch_dereplicate-sequences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_dereplicate-sequences.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,73 @@
+
+
+ Dereplicate sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_vsearch_fastq-stats.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_fastq-stats.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,72 @@
+
+
+ Fastq stats with vsearch.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_vsearch_join-pairs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_join-pairs.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,137 @@
+
+
+ Join paired-end reads.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_vsearch_uchime-denovo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_uchime-denovo.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,100 @@
+
+
+ De novo chimera filtering with vsearch.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r c28331a63dfd -r 3ba9833030c1 qiime2/qiime_vsearch_uchime-ref.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_uchime-ref.xml Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,110 @@
+
+
+ Reference-based chimera filtering with vsearch.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file