# HG changeset patch
# User florianbegusch
# Date 1527153667 14400
# Node ID 51b9b6b57732b132723fec7efeb8d54c975ba0f2
Uploaded
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,34 @@
+
+
+ - Merge features and taxonomy into a single biom file.
+
+ qiime2
+
+
+mkdir out;
+
+qiime tools export --output-dir out $taxonomy_qza;
+qiime tools export --output-dir out $biom_qza;
+
+sed -i '1s;^;#;' out/*.tsv;
+sed -i 's/Confidence/confidence/g' out/*.tsv;
+sed -i 's/Taxon/taxonomy/g' out/*.tsv;
+sed -i 's/Feature ID/OTU ID/g' out/*.tsv;
+
+biom add-metadata -i out/*.biom -o table_with_sample_metadata.biom --observation-metadata-fp out/*.tsv
+;
+mv *.biom $biom_and_tax_merged
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_alignment_mafft.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mafft.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,53 @@
+
+
+ - De novo multiple sequence alignment with MAFFT
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_alignment_mask.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mask.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,72 @@
+
+
+ - Positional conservation and gap filtering.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_citation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_citation.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,21 @@
+
+
+
+
+ @article{Caporaso_2010,
+ title={QIIME allows analysis of high-throughput community sequencing data},
+ volume={7},
+ ISSN={1548-7105},
+ DOI={10.1038/nmeth.f.303},
+ url={https://qiime2.org/},
+ number={5},
+ journal={Nature Methods},
+ publisher={Springer Nature},
+ author={Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K and Fierer, Noah and Pena, Antonio Gonzalez and Goodrich, Julia K and Gordon, Jeffrey I and et al.},
+ year={2010},
+ month={Apr},
+ pages={335-336}
+ }
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_composition_add-pseudocount.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_composition_add-pseudocount.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,55 @@
+
+
+ - Add pseudocount to table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_composition_ancom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_composition_ancom.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,94 @@
+
+
+ - Apply ANCOM to identify features that differ in abundance.
+
+ qiime2
+
+
+
+
+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_cutadapt_demux-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_demux-paired.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,82 @@
+
+
+ - Demultiplex paired-end sequence data with barcodes in- sequence.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_cutadapt_demux-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_demux-single.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,81 @@
+
+
+ - Demultiplex single-end sequence data with barcodes in- sequence.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
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+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_cutadapt_trim-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_trim-paired.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,186 @@
+
+
+ - Find and remove adapters in demultiplexed paired-end sequences.
+
+ qiime2
+
+
+
+
+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_cutadapt_trim-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_trim-single.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,145 @@
+
+
+ - Find and remove adapters in demultiplexed single-end sequences.
+
+ qiime2
+
+
+
+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_dada2_denoise-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_dada2_denoise-paired.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,176 @@
+
+
+ - Denoise and dereplicate paired-end sequences
+
+ qiime2
+
+
+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_dada2_denoise-pyro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_dada2_denoise-pyro.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,168 @@
+
+
+ - Denoise and dereplicate single-end pyrosequences
+
+ qiime2
+
+
+
+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_dada2_denoise-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_dada2_denoise-single.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,146 @@
+
+
+ - Denoise and dereplicate single-end sequences
+
+ qiime2
+
+
+
+
+
+
+
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+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_deblur_denoise-16S.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_deblur_denoise-16S.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,125 @@
+
+
+ - Deblur sequences using a 16S positive filter.
+
+ qiime2
+
+
+
+
+
+
+
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+
+
+
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+
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+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_deblur_denoise-other.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_deblur_denoise-other.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,126 @@
+
+
+ - Deblur sequences using a user-specified positive filter.
+
+ qiime2
+
+
+
+
+
+
+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_deblur_visualize-stats.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_deblur_visualize-stats.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,48 @@
+
+
+ - Visualize Deblur stats per sample.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_demux_emp-paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_emp-paired.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,84 @@
+
+
+ - Demultiplex paired-end sequence data generated with the EMP protocol.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_demux_emp-single.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_emp-single.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,83 @@
+
+
+ - Demultiplex sequence data generated with the EMP protocol.
+
+ qiime2
+
+
+
+
+
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+ qiime_citation.xml
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+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_demux_summarize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_summarize.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,60 @@
+
+
+ - Summarize counts per sample.
+
+ qiime2
+
+
+
+
+
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+
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+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_alpha-correlation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-correlation.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,75 @@
+
+
+ - Alpha diversity correlation
+
+ qiime2
+
+
+
+
+
+
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+
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+
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+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,61 @@
+
+
+ - Alpha diversity comparisons
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_alpha-phylogenetic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-phylogenetic.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,59 @@
+
+
+ - Alpha diversity (phylogenetic)
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_alpha-rarefaction.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha-rarefaction.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,137 @@
+
+
+ - Alpha rarefaction curves
+
+ qiime2
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_alpha.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_alpha.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,83 @@
+
+
+ - Alpha diversity
+
+ qiime2
+
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,95 @@
+
+
+ - Beta diversity group significance
+
+ qiime2
+
+
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,112 @@
+
+
+ - Beta diversity (phylogenetic) - High Performance Computation
+
+ qiime2
+
+
+
+
+
+
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+ qiime_citation.xml
+
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diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_beta-phylogenetic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta-phylogenetic.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,67 @@
+
+
+ - Beta diversity (phylogenetic)
+
+ qiime2
+
+
+
+
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+
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+
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+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_beta-rarefaction.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta-rarefaction.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,176 @@
+
+
+ - Beta diversity rarefaction
+
+ qiime2
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_beta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_beta.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,81 @@
+
+
+ - Beta diversity
+
+ qiime2
+
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_bioenv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_bioenv.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,67 @@
+
+
+ - bioenv
+
+ qiime2
+
+
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+
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+ qiime_citation.xml
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+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,162 @@
+
+
+ - Core diversity metrics (phylogenetic and non- phylogenetic)
+
+ qiime2
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_core-metrics.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_core-metrics.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,119 @@
+
+
+ - Core diversity metrics (non-phylogenetic)
+
+ qiime2
+
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+ qiime_citation.xml
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+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,92 @@
+
+
+ - Filter samples from a distance matrix.
+
+ qiime2
+
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_mantel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_mantel.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,103 @@
+
+
+ - Apply the Mantel test to two distance matrices
+
+ qiime2
+
+
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+
+
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+ qiime_citation.xml
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diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_pcoa.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_pcoa.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,46 @@
+
+
+ - Principal Coordinate Analysis
+
+ qiime2
+
+
+
+
+
+
+
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+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_diversity_procrustes-analysis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_procrustes-analysis.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,62 @@
+
+
+ - Procrustes Analysis
+
+ qiime2
+
+
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+ qiime_citation.xml
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+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_emperor_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_emperor_plot.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,71 @@
+
+
+ - Visualize and Interact with Principal Coordinates Analysis Plots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_emperor_procrustes-plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_emperor_procrustes-plot.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,79 @@
+
+
+ - Visualize and Interact with a procrustes plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,127 @@
+
+
+ - BLAST+ consensus taxonomy classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,124 @@
+
+
+ - VSEARCH consensus taxonomy classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,106 @@
+
+
+ - Pre-fitted sklearn-based taxonomy classifier
+
+ qiime2
+
+ = 0.0:
+ --p-confidence=$pconfidence
+ #end if
+ #end if
+
+ #if str($preadorientation) != 'None':
+ --p-read-orientation=$preadorientation
+ #end if
+
+ #if str($cmdconfig) != 'None':
+ --cmd-config=$cmdconfig
+ #end if
+
+ #set $pnjobs = '${GALAXY_SLOTS:-4}'
+ --p-n-jobs="$pnjobs"
+ --o-classification=oclassification;
+
+ cp oclassification.qza $oclassification;
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,72 @@
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,270 @@
+
+
+ - Train the naive_bayes classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,84 @@
+
+
+ - Train an almost arbitrary scikit-learn classifier
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,80 @@
+
+
+ - Identify core features in table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,133 @@
+
+
+ - Filter features from table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,125 @@
+
+
+ - Filter samples from table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,104 @@
+
+
+ - Filter features from sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_feature-table_group.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_group.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,96 @@
+
+
+ - Group samples or features by a metadata column
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_feature-table_heatmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_heatmap.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,353 @@
+
+
+ - Generate a heatmap representation of a feature table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,62 @@
+
+
+ - Combine collections of feature sequences
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,64 @@
+
+
+ - Combine collections of feature taxonomies
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_feature-table_merge.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_merge.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,73 @@
+
+
+ - Combine multiple tables
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,49 @@
+
+
+ - Convert to presence/absence
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_feature-table_rarefy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_rarefy.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,54 @@
+
+
+ - Rarefy table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,53 @@
+
+
+ - Convert to relative frequencies
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_feature-table_subsample.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_subsample.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,68 @@
+
+
+ - Subsample table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_feature-table_summarize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_summarize.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,67 @@
+
+
+ - Summarize table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,51 @@
+
+
+ - View sequence associated with each feature
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_add-pseudocount.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_add-pseudocount.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,55 @@
+
+
+ - Add pseudocount to table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_assign-ids.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_assign-ids.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,57 @@
+
+
+ - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_balance-taxonomy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_balance-taxonomy.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,131 @@
+
+
+ - Balance Summary
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_correlation-clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_correlation-clustering.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,54 @@
+
+
+ - Hierarchical clustering using feature correlation.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_dendrogram-heatmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_dendrogram-heatmap.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,185 @@
+
+
+ - Dendrogram heatmap.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_gradient-clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_gradient-clustering.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,83 @@
+
+
+ - Hierarchical clustering using gradient information.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_ilr-transform.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_ilr-transform.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,56 @@
+
+
+ - Isometric Log-ratio Transform
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_lme-regression.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_lme-regression.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,79 @@
+
+
+ - Simplicial Linear mixed effects regression
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_gneiss_ols-regression.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_ols-regression.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,83 @@
+
+
+ - Simplicial Ordinary Least Squares Regression
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_longitudinal_first-differences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_first-differences.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,132 @@
+
+
+ - Compute first differences or difference from baseline between sequential states
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_longitudinal_first-distances.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_first-distances.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,119 @@
+
+
+ - Compute first distances or distance from baseline between sequential states
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,156 @@
+
+
+ - Linear mixed effects modeling
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_longitudinal_nmit.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_nmit.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,99 @@
+
+
+ - Nonparametric microbial interdependence test
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_longitudinal_pairwise-differences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_pairwise-differences.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,164 @@
+
+
+ - Paired difference testing and boxplots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_longitudinal_pairwise-distances.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_pairwise-distances.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,156 @@
+
+
+ - Paired pairwise distance testing and boxplots
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_longitudinal_volatility.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_volatility.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,115 @@
+
+
+ - Volatility analysis
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_metadata_distance-matrix.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_metadata_distance-matrix.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,63 @@
+
+
+ - Create a distance matrix from a numeric Metadata column
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_metadata_tabulate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_metadata_tabulate.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,70 @@
+
+
+ - Interactively explore Metadata in an HTML table
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_phylogeny_fasttree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_fasttree.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,52 @@
+
+
+ - Construct a phylogenetic tree with FastTree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_phylogeny_filter-table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_filter-table.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,53 @@
+
+
+ - Remove features from table if they're not present in tree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_phylogeny_midpoint-root.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_phylogeny_midpoint-root.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,48 @@
+
+
+ - Midpoint root an unrooted phylogenetic tree.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,209 @@
+
+
+ - Evaluate expected vs. observed taxonomic composition of samples
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,76 @@
+
+
+ - Compare query (observed) vs. reference (expected) sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,110 @@
+
+
+ - Exclude sequences by alignment
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,88 @@
+
+
+ - Quality filter based on joined sequence quality scores.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,88 @@
+
+
+ - Quality filter based on sequence quality scores.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,205 @@
+
+
+ - Supervised learning classifier.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,203 @@
+
+
+ - Microbial maturity index prediction.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,179 @@
+
+
+ - Supervised learning regressor.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_taxa_barplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_barplot.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,97 @@
+
+
+ - Visualize taxonomy with an interactive bar plot
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_taxa_collapse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_collapse.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,86 @@
+
+
+ - Collapse features by their taxonomy at the specified level
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_taxa_filter-seqs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_filter-seqs.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,128 @@
+
+
+ - Taxonomy-based feature sequence filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_taxa_filter-table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_filter-table.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,130 @@
+
+
+ - Taxonomy-based feature table filter.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_tools_export.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_export.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,30 @@
+
+
+ - Export data from a QIIME 2 Artifact or Visualization.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_tools_export_collection.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_export_collection.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,22 @@
+
+
+ - Export data from a QIIME 2 Artifact or Visualization.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,22 @@
+
+
+ - Export data from a QIIME 2 Artifact or Visualization.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_tools_import.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_tools_import.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,257 @@
+
+
+ - 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
+
+#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]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,101 @@
+
+
+ - Closed-reference clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,78 @@
+
+
+ - De novo clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 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 Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,111 @@
+
+
+ - Open-reference clustering of features.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_vsearch_dereplicate-sequences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_dereplicate-sequences.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,57 @@
+
+
+ - Dereplicate sequences.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_vsearch_join-pairs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_join-pairs.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,156 @@
+
+
+ - Join paired-end reads.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
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+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_vsearch_uchime-denovo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_uchime-denovo.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,103 @@
+
+
+ - De novo chimera filtering with vsearch.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 qiime2/qiime_vsearch_uchime-ref.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_uchime-ref.xml Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,113 @@
+
+
+ - Reference-based chimera filtering with vsearch.
+
+ qiime2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ qiime_citation.xml
+
+
+
diff -r 000000000000 -r 51b9b6b57732 tool_data/ref_classifier.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/ref_classifier.loc Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,5 @@
+#
+#
+#For each reference database, you need to download the qza file in qiime path
+#
+
diff -r 000000000000 -r 51b9b6b57732 tool_data/ref_taxnonomy.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/ref_taxnonomy.loc Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,5 @@
+#
+#
+#For each reference database, you need to download the qza file in qiime path
+#
+
diff -r 000000000000 -r 51b9b6b57732 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,11 @@
+
+
+ value, name, dbkey, path
+
+
+
+ value, name, dbkey, path
+
+
+
+