Repository revision
3:a3613553c65f

Repository 'poppunk'
hg clone https://toolshed.g2.bx.psu.edu/repos/johnlees/poppunk

PopPUNK (cluster) tool metadata
Miscellaneous
Cluster bacterial genomes
poppunk_cluster
toolshed.g2.bx.psu.edu/repos/johnlees/poppunk/poppunk_cluster/1.1.6
1.1.6
poppunk --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/johnlees/poppunk/poppunk_cluster/1.1.6 (this tool)
poppunk_cluster
Requirements (dependencies defined in the <requirements> tag set)
name version type
poppunk 1.1.6 package
Additional information about this tool
##Set up input files
       ##echo "$input_assemblies" | tr ',' '\n' > 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

       
None
False
False
Functional tests
name inputs outputs required files
Test-1 viz|microreact: False
input_assemblies: [u'12673_8_24.contigs_velvet.fa', u'12673_8_34.contigs_velvet.fa', u'12673_8_43.contigs_velvet.fa', u'12754_4_71.contigs_velvet.fa', u'12754_4_77.contigs_velvet.fa']
model|model_mode: gmm
no_full_db: False
model|K: 4
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
12673_8_24.contigs_velvet.fa
12673_8_34.contigs_velvet.fa
12673_8_43.contigs_velvet.fa
12754_4_71.contigs_velvet.fa
12754_4_77.contigs_velvet.fa
name