# HG changeset patch
# User johnlees
# Date 1558019289 14400
# Node ID 1d7ba8646dd17253dd2238a726e09258b0054aeb
# Parent 88ea7ea4b3d2b068caae1f8138be5fa03e6c2fde
planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Thu May 16 11:08:09 2019 -0400
@@ -0,0 +1,201 @@
+ Apache License
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diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu May 16 11:08:09 2019 -0400
@@ -0,0 +1,2 @@
+# PopPUNK_galaxy
+Galaxy tool for PopPUNK
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 clusters.csv
--- a/clusters.csv Wed May 15 14:58:24 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-Taxon,Cluster
-12754_4_77.contigs_velvet.fa,1
-12673_8_34.contigs_velvet.fa,1
-12673_8_43.contigs_velvet.fa,1
-12673_8_24.contigs_velvet.fa,1
-12754_4_71.contigs_velvet.fa,2
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 poppunk_cluster.xml
--- a/poppunk_cluster.xml Wed May 15 14:58:24 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,284 +0,0 @@
-
- Cluster bacterial genomes
-
-
- poppunk
-
-
-
-
- r_files.txt
- #for $input in $input_assemblies
- ln -s $input $input.element_identifier && echo $input.element_identifier >> r_files.txt;
- #end for
-
- ## command line 1 (create db)
- echo "
- poppunk
- --create-db
- --r-files r_files.txt
- --output poppunk_db
- --threads \${GALAXY_SLOTS:-1}
- --min-k $min_k
- --max-k $max_k
- --k-step $k_step
- --sketch-size $sketch_size
- --max-a-dist $max_a_dist
- #if $ignore_length
- --ignore_length
- #end if
- --no-stream
- " > poppunk_1.sh
-
- && sh poppunk_1.sh
-
- ## command line 2 (fit model)
- && echo "
- poppunk
- --fit-model
- --distances poppunk_db/poppunk_db.dists
- --ref-db poppunk_db
- --output poppunk_db
-
- ## mode
- #if str( $model.model_mode ) == "gmm":
- --K ${model.K}
- #end if
- #if str( $model.model_mode ) == "dbscan":
- --dbscan
- --D $model.D
- --min-cluster-prop $model.min_cluster_prop
- #end if
-
- #if not $no_full_db or $refine.refine_model
- --full-db
- #end if
-
- #if not $refine.refine_model:
- #if $external_clusters
- --external-clustering $external_clusters
- #end if
-
- ## viz
- #if $cytoscape:
- --cytoscape
- #end if
- #if $viz.microreact:
- --microreact
- --rapidnj rapidnj
- --perplexity $viz.perplexity
- #end if
- #if ($cytoscape or $viz.microreact) and $info_csv:
- --info-csv $info_csv
- #end if
- #end if
-
- " > poppunk_2.sh
-
- && sh poppunk_2.sh
-
- ## command line 3 (refine)
- #if $refine.refine_model:
- && echo "
- poppunk
- --refine-model
- --distances poppunk_db/poppunk_db.dists
- --ref-db poppunk_db
- --output poppunk_db
- --threads \${GALAXY_SLOTS:-1}
- --pos-shift $refine.pos_shift
- --neg-shift $refine.neg_shift
-
- #if not $no_full_db
- --full-db
- #end if
-
- #if $external_clusters
- --external-clustering $external_clusters
- #end if
-
- ## viz
- #if $cytoscape:
- --cytoscape
- #end if
- #if $viz.microreact:
- --microreact
- --rapidnj rapidnj
- --perplexity $viz.perplexity
- #end if
- #if ($cytoscape or $viz.microreact) and $info_csv:
- --info-csv $info_csv
- #end if
-
- " > poppunk_3.sh
-
- && sh poppunk_3.sh;
- #end if
-
- ]]>
-
-
-
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- no_full_db == True
-
-
- model['model_mode'] == 'gmm'
-
-
- model['model_mode'] == 'gmm'
-
-
- model['model_mode'] == 'dbscan'
-
-
- refine['refine_model'] == True
-
-
- cytoscape == True
-
-
- cytoscape == True
-
-
- viz['microreact'] == True
-
-
- viz['microreact'] == True
-
-
- viz['microreact'] == True
-
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-@article{Lees01022019,
- author = {Lees, John A. and Harris, Simon R. and Tonkin-Hill, Gerry and Gladstone, Rebecca A. and Lo, Stephanie W. and Weiser, Jeffrey N. and Corander, Jukka and Bentley, Stephen D. and Croucher, Nicholas J.},
- title = {Fast and flexible bacterial genomic epidemiology with PopPUNK},
- volume = {29},
- number = {2},
- pages = {304-316},
- year = {2019},
- doi = {10.1101/gr.241455.118},
- abstract ={The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K-mers), a software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates’ divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using data from both simulations and genomic collections representing 10 taxonomically widespread species. Connections between closely related isolates of the same strain are robustly identified, despite interspecies variation in the pairwise distance distributions that reflects species’ diverse evolutionary patterns. PopPUNK can process 103–104 genomes in a single batch, with minimal memory use and runtimes up to 200-fold faster than existing model-based methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to reanalyze all genomes de novo. This facilitates real-time surveillance with consistent cluster naming between studies and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualization and online publication is streamlined through the automatic output of results to multiple platforms. PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.},
- URL = {http://genome.cshlp.org/content/29/2/304.abstract},
- eprint = {http://genome.cshlp.org/content/29/2/304.full.pdf+html},
- journal = {Genome Research}
- }
-
-
diff -r 88ea7ea4b3d2 -r 1d7ba8646dd1 tools/PopPUNK/poppunk_cluster.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/PopPUNK/poppunk_cluster.xml Thu May 16 11:08:09 2019 -0400
@@ -0,0 +1,284 @@
+
+ Cluster bacterial genomes
+
+
+ poppunk
+
+
+
+
+ r_files.txt
+ #for $input in $input_assemblies
+ ln -s $input $input.element_identifier && echo $input.element_identifier >> r_files.txt;
+ #end for
+
+ ## command line 1 (create db)
+ echo "
+ poppunk
+ --create-db
+ --r-files r_files.txt
+ --output poppunk_db
+ --threads \${GALAXY_SLOTS:-1}
+ --min-k $min_k
+ --max-k $max_k
+ --k-step $k_step
+ --sketch-size $sketch_size
+ --max-a-dist $max_a_dist
+ #if $ignore_length
+ --ignore_length
+ #end if
+ --no-stream
+ " > poppunk_1.sh
+
+ && sh poppunk_1.sh
+
+ ## command line 2 (fit model)
+ && echo "
+ poppunk
+ --fit-model
+ --distances poppunk_db/poppunk_db.dists
+ --ref-db poppunk_db
+ --output poppunk_db
+
+ ## mode
+ #if str( $model.model_mode ) == "gmm":
+ --K ${model.K}
+ #end if
+ #if str( $model.model_mode ) == "dbscan":
+ --dbscan
+ --D $model.D
+ --min-cluster-prop $model.min_cluster_prop
+ #end if
+
+ #if not $no_full_db or $refine.refine_model
+ --full-db
+ #end if
+
+ #if not $refine.refine_model:
+ #if $external_clusters
+ --external-clustering $external_clusters
+ #end if
+
+ ## viz
+ #if $cytoscape:
+ --cytoscape
+ #end if
+ #if $viz.microreact:
+ --microreact
+ --rapidnj rapidnj
+ --perplexity $viz.perplexity
+ #end if
+ #if ($cytoscape or $viz.microreact) and $info_csv:
+ --info-csv $info_csv
+ #end if
+ #end if
+
+ " > poppunk_2.sh
+
+ && sh poppunk_2.sh
+
+ ## command line 3 (refine)
+ #if $refine.refine_model:
+ && echo "
+ poppunk
+ --refine-model
+ --distances poppunk_db/poppunk_db.dists
+ --ref-db poppunk_db
+ --output poppunk_db
+ --threads \${GALAXY_SLOTS:-1}
+ --pos-shift $refine.pos_shift
+ --neg-shift $refine.neg_shift
+
+ #if not $no_full_db
+ --full-db
+ #end if
+
+ #if $external_clusters
+ --external-clustering $external_clusters
+ #end if
+
+ ## viz
+ #if $cytoscape:
+ --cytoscape
+ #end if
+ #if $viz.microreact:
+ --microreact
+ --rapidnj rapidnj
+ --perplexity $viz.perplexity
+ #end if
+ #if ($cytoscape or $viz.microreact) and $info_csv:
+ --info-csv $info_csv
+ #end if
+
+ " > poppunk_3.sh
+
+ && sh poppunk_3.sh;
+ #end if
+
+ ]]>
+
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+ no_full_db == True
+
+
+ model['model_mode'] == 'gmm'
+
+
+ model['model_mode'] == 'gmm'
+
+
+ model['model_mode'] == 'dbscan'
+
+
+ refine['refine_model'] == True
+
+
+ cytoscape == True
+
+
+ cytoscape == True
+
+
+ viz['microreact'] == True
+
+
+ viz['microreact'] == True
+
+
+ viz['microreact'] == True
+
+
+
+
+
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+
+@article{Lees01022019,
+ author = {Lees, John A. and Harris, Simon R. and Tonkin-Hill, Gerry and Gladstone, Rebecca A. and Lo, Stephanie W. and Weiser, Jeffrey N. and Corander, Jukka and Bentley, Stephen D. and Croucher, Nicholas J.},
+ title = {Fast and flexible bacterial genomic epidemiology with PopPUNK},
+ volume = {29},
+ number = {2},
+ pages = {304-316},
+ year = {2019},
+ doi = {10.1101/gr.241455.118},
+ abstract ={The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K-mers), a software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates’ divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using data from both simulations and genomic collections representing 10 taxonomically widespread species. Connections between closely related isolates of the same strain are robustly identified, despite interspecies variation in the pairwise distance distributions that reflects species’ diverse evolutionary patterns. PopPUNK can process 103–104 genomes in a single batch, with minimal memory use and runtimes up to 200-fold faster than existing model-based methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to reanalyze all genomes de novo. This facilitates real-time surveillance with consistent cluster naming between studies and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualization and online publication is streamlined through the automatic output of results to multiple platforms. PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.},
+ URL = {http://genome.cshlp.org/content/29/2/304.abstract},
+ eprint = {http://genome.cshlp.org/content/29/2/304.full.pdf+html},
+ journal = {Genome Research}
+ }
+
+