qiime: pick_otus.xml annotate

author	bebatut
date	Tue, 02 Feb 2016 05:50:37 -0500
parents
children

rev	line source
0 c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	1 <tool id="qiime_pick_otus" name="pick otus" version="1.9.1galaxy1">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	2
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	3 <description>OTU picking</description>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	4
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	5 <macros>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	6 <import>macros.xml</import>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	7 </macros>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	8
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	9 <expand macro="requirements" />
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	10
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	11 <command>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	12 <![CDATA[
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	13 pick_otus.py
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	14 -i $input_seqs_filepath
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	15 -o fastasplit
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	16
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	17 #if str($methode.otu_picking_method) != 'None':
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	18 -m $methode.otu_picking_method
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	19 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	20
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	21 #if str($methode.otu_picking_method) in ("uclust_ref","usearch_ref") :
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	22 -r $methode.refseqs_fp
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	23 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	24
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	25 #if str($methode.otu_picking_method) in ("uclust","uclust_ref","usearch","usearch_ref","sumaclust") :
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	26 #if $methode.similarity:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	27 -s $methode.similarity
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	28 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	29 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	30
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	31 #if str($methode.otu_picking_method) == "sumaclust":
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	32 #if $methode.sumaclust_exact:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	33 --sumaclust_exact
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	34 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	35 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	36
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	37 #if str($methode.otu_picking_method) == "swarm":
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	38 #if $methode.swarm_resolution:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	39 --swarm_resolution=$methode.swarm_resolution
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	40 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	41 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	42
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	43 #if str($methode.otu_picking_method) in ("uclust","uclust_ref","usearch","usearch_ref"):
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	44 #if $methode.enable_rev_strand_match:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	45 -z
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	46 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	47 #if str($methode.max_accepts):
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	48 --max_accepts=$methode.max_accepts
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	49 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	50
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	51 #if str($methode.max_rejects):
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	52 --max_rejects=$methode.max_rejects
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	53 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	54 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	55
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	56 #if str($methode.otu_picking_method) in ("uclust","uclust_ref"):
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	57 #if $methode.stepwords:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	58 --stepwords=$methode.stepwords
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	59 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	60 #if $methode.suppress_presort_by_abundance_uclust:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	61 -D
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	62 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	63 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	64
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	65 #if str($methode.otu_picking_method) == "uclust":
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	66 #if $methode.optimal_uclust:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	67 -A
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	68 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	69 #if $methode.exact_uclust:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	70 -E
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	71 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	72 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	73
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	74 #if str($methode.otu_picking_method) == "usearch":
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	75 #if $methode.percent_id_err:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	76 -j $methode.percent_id_err
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	77 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	78 #if $methode.abundance_skew:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	79 -a $methode.abundance_skew
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	80 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	81 #if str($methode.db_filepath) != 'None':
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	82 -f $methode.db_filepath
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	83 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	84 #if $methode.perc_id_blast:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	85 --perc_id_blast=$methode.perc_id_blast
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	86 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	87 #if $methode.suppress_de_novo_chimera_detection:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	88 -k
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	89 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	90 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	91
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	92 #if str($methode.otu_picking_method) in ("sumaclust","swarm"):
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	93 #if str($methode.threads):
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	94 --threads=$methode.threads
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	95 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	96 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	97
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	98 #if $prefix_prefilter_length:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	99 -n $prefix_prefilter_length
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	100 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	101
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	102 #if $prefix_length:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	103 -p $prefix_length
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	104 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	105
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	106 #if $suffix_length:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	107 -u $suffix_length
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	108 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	109
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	110 #if str($non_chimeras_retention):
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	111 -F $non_chimeras_retention
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	112 #end if
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	113 ]]>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	114 </command>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	115
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	116 <inputs>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	117 <param label="-i/--input_seqs_filepath: Path to input sequences file"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	118 name="input_seqs_filepath" optional="False" type="data"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	119 <conditional name="methode">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	120 <param label="-m/--otu_picking_method: Method for picking OTUs. Valid
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	121 choices are: sortmerna, mothur, trie, uclust_ref, usearch, usearch_ref,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	122 blast, usearch61, usearch61_ref, sumaclust, swarm, prefix_suffix,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	123 cdhit, uclust. The mothur method requires an input file of aligned
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	124 sequences. usearch will enable the usearch quality filtering
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	125 pipeline. [default: uclust]" name="otu_picking_method"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	126 optional="FALSE" type="select">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	127 <option selected="True" value="uclust">uclust</option>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	128 <option value="uclust_ref">uclust_ref</option>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	129 <option value="usearch">usearch</option>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	130 <option value="usearch_ref">usearch_ref</option>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	131 <option value="sumaclust">sumaclust</option>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	132 <option value="swarm">swarm</option>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	133 </param>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	134 <when value="uclust_ref">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	135 <param default="/home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	136 label="-r/--refseqs_fp: Path to reference sequences to search
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	137 against when using -m uclust_ref, -m usearch_ref [default:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	138 /home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta]" name="refseqs_fp" optional="True" type="data"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	139 <param default="0.97" label="-s/--similarity: Sequence similarity
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	140 threshold (for blast, cdhit, uclust, uclust_ref, usearch,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	141 usearch_ref, usearch61, usearch61_ref, sumaclust or sortmerna
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	142 [default: 0.97]" name="similarity" optional="True" type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	143 <param label="-z/--enable_rev_strand_match: Enable reverse strand
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	144 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	145 or usearch61_ref otu picking, will double the amount of memory
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	146 used. [default: False]" name="enable_rev_strand_match"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	147 selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	148 <param label="-D/--suppress_presort_by_abundance_uclust: Suppress
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	149 presorting of sequences by abundance when picking OTUs with
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	150 uclust or uclust_ref [default: False]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	151 name="suppress_presort_by_abundance_uclust" selected="False"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	152 type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	153 <param label="-C/--suppress_new_clusters: Suppress creation of new
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	154 clusters using seqs that don't match reference when using -m
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	155 uclust_ref, -m usearch61_ref, or -m usearch_ref [default: False]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	156 name="suppress_new_clusters" selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	157 <param default="default" label="--max_accepts: max_accepts value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	158 to uclust, uclust_ref, usearch61, and usearch61_ref. By default,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	159 will use value suggested by method (uclust: 1, usearch61: 1)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	160 [default: default]" name="max_accepts" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	161 <param default="default" label="--max_rejects: max_rejects value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	162 for uclust, uclust_ref, usearch61, and usearch61_ref. With
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	163 default settings, will use value recommended by clustering
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	164 method used (uclust: 8, usearch61: 8 for usearch_fast_cluster
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	165 option, 32 for reference and smallmem options) [default:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	166 default]" name="max_rejects" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	167 <param default="8" label="--stepwords: stepwords value to uclust
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	168 and uclust_ref [default: 8]" name="stepwords" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	169 type="integer"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	170 </when>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	171 <when value="usearch_ref">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	172 <param default="/home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	173 label="-r/--refseqs_fp: Path to reference sequences to search
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	174 against when using -m blast, -m sortmerna, -m uclust_ref, -m
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	175 usearch_ref, or -m usearch61_ref [default:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	176 /home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta]" name="refseqs_fp" optional="True" type="data"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	177 <param default="0.97" label="-s/--similarity: Sequence similarity
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	178 threshold (for blast, cdhit, uclust, uclust_ref, usearch,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	179 usearch_ref, usearch61, usearch61_ref, sumaclust or sortmerna
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	180 [default: 0.97]" name="similarity" optional="True" type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	181 <param label="-z/--enable_rev_strand_match: Enable reverse strand
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	182 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	183 or usearch61_ref otu picking, will double the amount of memory
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	184 used. [default: False]" name="enable_rev_strand_match" selected="False"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	185 type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	186 <param label="-C/--suppress_new_clusters: Suppress creation of new
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	187 clusters using seqs that don't match reference when using -m
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	188 uclust_ref, -m usearch61_ref, or -m usearch_ref [default: False]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	189 name="suppress_new_clusters" selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	190 <param default="default" label="--max_accepts: max_accepts value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	191 to uclust, uclust_ref, usearch61, and usearch61_ref. By default,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	192 will use value suggested by method (uclust: 1, usearch61: 1)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	193 [default: default]" name="max_accepts" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	194 <param default="default" label="--max_rejects: max_rejects value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	195 for uclust, uclust_ref, usearch61, and usearch61_ref. With
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	196 default settings, will use value recommended by clustering method
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	197 used (uclust: 8, usearch61: 8 for usearch_fast_cluster option,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	198 32 for reference and smallmem options) [default: default]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	199 name="max_rejects" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	200 </when>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	201 <when value="usearch">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	202 <param default="0.97" value="0.97" label="-s/--similarity: Sequence
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	203 similarity threshold (for blast, cdhit, uclust, uclust_ref,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	204 usearch, usearch_ref, usearch61, usearch61_ref, sumaclust or
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	205 sortmerna [default: 0.97]" name="similarity" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	206 type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	207 <param label="-z/--enable_rev_strand_match: Enable reverse strand
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	208 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	209 or usearch61_ref otu picking, will double the amount of memory
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	210 used. [default: False]" name="enable_rev_strand_match"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	211 selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	212 <param default="default" label="--max_accepts: max_accepts value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	213 to uclust, uclust_ref, usearch61, and usearch61_ref. By
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	214 default, will use value suggested by method (uclust: 1,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	215 usearch61: 1) [default: default]" name="max_accepts" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	216 type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	217 <param default="default" label="--max_rejects: max_rejects value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	218 for uclust, uclust_ref, usearch61, and usearch61_ref. With
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	219 default settings, will use value recommended by clustering
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	220 method used (uclust: 8, usearch61: 8 for usearch_fast_cluster
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	221 option, 32 for reference and smallmem options) [default: default]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	222 name="max_rejects" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	223 <param default="0.97" value="0.97" label="-j/--percent_id_err:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	224 Percent identity threshold for cluster error detection with
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	225 usearch, expressed as a fraction between 0 and 1. [default: 0.97]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	226 name="percent_id_err" optional="True" type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	227 <param default="2.0" label="-a/--abundance_skew: Abundance skew
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	228 setting for de novo chimera detection with usearch. [default: 2.0]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	229 name="abundance_skew" optional="True" type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	230 <param default="None" label="-f/--db_filepath: Reference database
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	231 of fasta sequences for reference based chimera detection with
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	232 usearch. [default: None]" name="db_filepath" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	233 type="data"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	234 <param default="0.97" value="0.97" label="--perc_id_blast: Percent
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	235 ID for mapping OTUs created by usearch back to original sequence
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	236 IDs [default: 0.97]" name="perc_id_blast" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	237 type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	238 <param label="-k/--suppress_de_novo_chimera_detection: Suppress
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	239 de novo chimera detection in usearch. [default: False]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	240 name="suppress_de_novo_chimera_detection" selected="False"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	241 type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	242 <param label="--usearch_fast_cluster: Use fast clustering option
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	243 for usearch or usearch61_ref with new clusters.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	244 --enable_rev_strand_match can not be enabled with this option,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	245 and the only valid option for usearch61_sort_method is 'length'.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	246 This option uses more memory than the default option for de novo
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	247 clustering. [default: False]" name="usearch_fast_cluster"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	248 selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	249 </when>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	250 <when value="sumaclust">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	251 <param default="0.97" value="0.97" label="-s/--similarity: Sequence
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	252 similarity threshold (for blast, cdhit, uclust, uclust_ref,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	253 usearch, usearch_ref, usearch61, usearch61_ref, sumaclust or
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	254 sortmerna [default: 0.97]" name="similarity" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	255 type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	256 <param label="--sumaclust_exact: A sequence is assigned to the best
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	257 matching seed rather than the first matching seed passing the
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	258 similarity threshold [default: False]" name="sumaclust_exact"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	259 selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	260 <param default="1" label="--threads: Specify number of threads (1
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	261 thread per core) to be used for usearch61, sortmerna, sumaclust and swarm commands that utilize multithreading. [default: 1]" name="threads" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	262 </when>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	263 <when value="swarm">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	264 <param default="1" label="--swarm_resolution: Maximum number of
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	265 differences allowed between two amplicons, meaning that two
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	266 amplicons will be grouped if they have integer (or less)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	267 differences (see Swarm manual at https://github.com/torognes/swarm
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	268 for more details). [default: 1]" name="swarm_resolution"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	269 optional="True" type="integer"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	270 <param default="1" label="--threads: Specify number of threads (1
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	271 thread per core) to be used for usearch61, sortmerna, sumaclust
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	272 and swarm commands that utilize multithreading. [default: 1]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	273 name="threads" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	274 </when>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	275 <when value="uclust">
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	276 <param default="0.97" value="0.97" label="-s/--similarity: Sequence
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	277 similarity threshold (for blast, cdhit, uclust, uclust_ref,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	278 usearch, usearch_ref, usearch61, usearch61_ref, sumaclust or
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	279 sortmerna [default: 0.97]" name="similarity" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	280 type="float"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	281 <param label="-z/--enable_rev_strand_match: Enable reverse strand
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	282 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	283 or usearch61_ref otu picking, will double the amount of memory
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	284 used. [default: False]" name="enable_rev_strand_match" selected="False"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	285 type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	286 <param label="-A/--optimal_uclust: Pass the --optimal flag to uclust
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	287 for uclust otu picking. [default: False]" name="optimal_uclust"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	288 selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	289 <param label="-D/--suppress_presort_by_abundance_uclust: Suppress
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	290 presorting of sequences by abundance when picking OTUs with
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	291 uclust or uclust_ref [default: False]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	292 name="suppress_presort_by_abundance_uclust" selected="False"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	293 type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	294 <param default="default" label="--max_accepts: max_accepts value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	295 to uclust, uclust_ref, usearch61, and usearch61_ref. By default,
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	296 will use value suggested by method (uclust: 1, usearch61: 1)
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	297 [default: default]" name="max_accepts" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	298 type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	299 <param default="default" label="--max_rejects: max_rejects value
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	300 for uclust, uclust_ref, usearch61, and usearch61_ref. With
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	301 default settings, will use value recommended by clustering
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	302 method used (uclust: 8, usearch61: 8 for usearch_fast_cluster
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	303 option, 32 for reference and smallmem options) [default: default]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	304 name="max_rejects" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	305 <param default="8" label="--stepwords: stepwords value to uclust
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	306 and uclust_ref [default: 8]" name="stepwords" optional="True"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	307 type="integer"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	308 <param label="-E/--exact_uclust: Pass the --exact flag to uclust
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	309 for uclust otu picking. [default: False]" name="exact_uclust"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	310 selected="False" type="boolean"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	311 </when>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	312 </conditional>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	313
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	314 <param default="None" label="-n/--prefix_prefilter_length: Prefilter data
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	315 so seqs with identical first prefix_prefilter_length are automatically
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	316 grouped into a single OTU. This is useful for large sequence collections
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	317 where OTU picking doesn't scale well [default: None; 100 is a good value]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	318 name="prefix_prefilter_length" optional="True" type="integer"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	319 <param default="50" label="-p/--prefix_length: Prefix length when using
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	320 the prefix_suffix otu picker; WARNING: CURRENTLY DIFFERENT FROM
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	321 prefix_prefilter_length (-n)! [default: 50]" name="prefix_length"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	322 optional="True" type="integer"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	323 <param default="50" label="-u/--suffix_length: Suffix length when using
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	324 the prefix_suffix otu picker [default: 50]" name="suffix_length"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	325 optional="True" type="integer"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	326 <param default="union" label="-F/--non_chimeras_retention: Selects subsets
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	327 of sequences detected as non-chimeras to retain after de novo and
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	328 reference based chimera detection. Options are intersection or union.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	329 union will retain sequences that are flagged as non-chimeric from either
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	330 filter, while intersection will retain only those sequences that are
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	331 flagged as non-chimeras from both detection methods. [default: union]"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	332 name="non_chimeras_retention" optional="True" type="text"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	333 </inputs>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	334 <outputs>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	335 <data format="txt" from_work_dir="fastasplit/*_otus.txt"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	336 name="pick_otus.txt" label="pick_otus.txt"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	337 <data format="txt" from_work_dir="fastasplit/*_otus.log"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	338 name="pick_otus.log" label="pick_otus.log"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	339 <data format="txt" from_work_dir="fastasplit/*_failures.txt"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	340 name="pick_otus_failures.txt" label="pick_otus_failures.txt"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	341 </outputs>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	342
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	343 <tests>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	344 <test>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	345 </test>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	346 </tests>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	347
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	348 <help><![CDATA[
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	349 What it does
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	350
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	351 The OTU picking step assigns similar sequences to operational taxonomic units, or OTUs, by clustering sequences based on a user-defined similarity threshold. Sequences which are similar at or above the threshold level are taken to represent the presence of a taxonomic unit (e.g., a genus, when the similarity threshold is set at 0.94) in the sequence collection.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	352
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	353 Currently, the following clustering methods have been implemented in QIIME:
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	354
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	355 1. uclust, creates "seeds" of sequences which generate clusters based on percent identity.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	356
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	357 2. uclust_ref, as uclust, but takes a reference database to use as seeds. New clusters can be toggled on or off.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	358
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	359 3. usearch, creates "seeds" of sequences which generate clusters based on percent identity, filters low abundance clusters, performs de novo and reference based chimera detection.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	360
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	361 4. usearch_ref, as usearch, but takes a reference database to use as seeds. New clusters can be toggled on or off.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	362
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	363 5. sumaclust, creates "seeds" of sequences which generate clusters based on similarity threshold.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	364
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	365 6. swarm, creates "seeds" of sequences which generate clusters based on a resolution threshold.
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	368 Chimera checking with usearch 6.X is implemented in identify_chimeric_seqs.py. Chimera checking should be done first with usearch 6.X, and the filtered resulting fasta file can then be clustered.
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	371 The primary inputs for pick_otus.py are:
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	375 2. An OTU threshold (default is 0.97, roughly corresponding to species-level OTUs);
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	377 3. The method to be applied for clustering sequences into OTUs.
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	379 pick_otus.py takes a standard fasta file as input.
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	381
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	382 The output consists of two files (i.e. seqs_otus.txt and seqs_otus.log). The .txt file is composed of tab-delimited lines, where the first field on each line corresponds to an (arbitrary) cluster identifier, and the remaining fields correspond to sequence identifiers assigned to that cluster. Sequence identifiers correspond to those provided in the input FASTA file. Usearch (i.e. usearch quality filter) can additionally have log files for each intermediate call to usearch.
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	393 This result implies that four clusters were created based on 7 input sequences.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	394 The first cluster (cluster id 0) contains two sequences, sequence ids seq1 and
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	395 seq5; the second cluster (cluster id 1) contains one sequence, sequence id seq2;
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	396 the third cluster (cluster id 2) contains one sequence, sequence id seq3, and the
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	397 final cluster (cluster id 3) contains three sequences, sequence ids seq4, seq6,
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	400 The resulting .log file contains a list of parameters passed to the pick_otus.py
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	401 script along with the output location of the resulting .txt file.</help>
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty bebatut parents: diff changeset	410 <citation type="doi">10.7287/peerj.preprints.386v1/supp-1</citation>
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0

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1 <tool id="qiime_pick_otus" name="pick otus" version="1.9.1galaxy1">

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2

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3 <description>OTU picking</description>

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4

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5 <macros>

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6 <import>macros.xml</import>

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7 </macros>

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8

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9 <expand macro="requirements" />

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10

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11 <command>

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12 <![CDATA[

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13 pick_otus.py

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14 -i $input_seqs_filepath

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15 -o fastasplit

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16

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17 #if str($methode.otu_picking_method) != 'None':

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18 -m $methode.otu_picking_method

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19 #end if

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20

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21 #if str($methode.otu_picking_method) in ("uclust_ref","usearch_ref") :

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22 -r $methode.refseqs_fp

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23 #end if

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24

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25 #if str($methode.otu_picking_method) in ("uclust","uclust_ref","usearch","usearch_ref","sumaclust") :

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26 #if $methode.similarity:

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27 -s $methode.similarity

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28 #end if

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29 #end if

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30

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31 #if str($methode.otu_picking_method) == "sumaclust":

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32 #if $methode.sumaclust_exact:

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33 --sumaclust_exact

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34 #end if

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35 #end if

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36

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37 #if str($methode.otu_picking_method) == "swarm":

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38 #if $methode.swarm_resolution:

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39 --swarm_resolution=$methode.swarm_resolution

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40 #end if

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41 #end if

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42

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43 #if str($methode.otu_picking_method) in ("uclust","uclust_ref","usearch","usearch_ref"):

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44 #if $methode.enable_rev_strand_match:

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45 -z

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46 #end if

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47 #if str($methode.max_accepts):

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48 --max_accepts=$methode.max_accepts

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49 #end if

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50

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51 #if str($methode.max_rejects):

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52 --max_rejects=$methode.max_rejects

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53 #end if

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54 #end if

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55

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56 #if str($methode.otu_picking_method) in ("uclust","uclust_ref"):

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57 #if $methode.stepwords:

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58 --stepwords=$methode.stepwords

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59 #end if

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60 #if $methode.suppress_presort_by_abundance_uclust:

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61 -D

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62 #end if

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63 #end if

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64

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65 #if str($methode.otu_picking_method) == "uclust":

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66 #if $methode.optimal_uclust:

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67 -A

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68 #end if

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69 #if $methode.exact_uclust:

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70 -E

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71 #end if

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72 #end if

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73

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74 #if str($methode.otu_picking_method) == "usearch":

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75 #if $methode.percent_id_err:

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76 -j $methode.percent_id_err

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77 #end if

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78 #if $methode.abundance_skew:

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79 -a $methode.abundance_skew

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80 #end if

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81 #if str($methode.db_filepath) != 'None':

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82 -f $methode.db_filepath

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83 #end if

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84 #if $methode.perc_id_blast:

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85 --perc_id_blast=$methode.perc_id_blast

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86 #end if

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87 #if $methode.suppress_de_novo_chimera_detection:

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88 -k

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89 #end if

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90 #end if

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91

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92 #if str($methode.otu_picking_method) in ("sumaclust","swarm"):

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93 #if str($methode.threads):

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94 --threads=$methode.threads

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95 #end if

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96 #end if

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97

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98 #if $prefix_prefilter_length:

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99 -n $prefix_prefilter_length

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100 #end if

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101

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102 #if $prefix_length:

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103 -p $prefix_length

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104 #end if

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105

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106 #if $suffix_length:

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107 -u $suffix_length

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108 #end if

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109

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110 #if str($non_chimeras_retention):

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111 -F $non_chimeras_retention

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112 #end if

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113 ]]>

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114 </command>

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115

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116 <inputs>

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117 <param label="-i/--input_seqs_filepath: Path to input sequences file"

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118 name="input_seqs_filepath" optional="False" type="data"/>

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119 <conditional name="methode">

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120 <param label="-m/--otu_picking_method: Method for picking OTUs. Valid

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121 choices are: sortmerna, mothur, trie, uclust_ref, usearch, usearch_ref,

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122 blast, usearch61, usearch61_ref, sumaclust, swarm, prefix_suffix,

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123 cdhit, uclust. The mothur method requires an input file of aligned

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124 sequences. usearch will enable the usearch quality filtering

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125 pipeline. [default: uclust]" name="otu_picking_method"

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126 optional="FALSE" type="select">

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127 <option selected="True" value="uclust">uclust</option>

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128 <option value="uclust_ref">uclust_ref</option>

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129 <option value="usearch">usearch</option>

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130 <option value="usearch_ref">usearch_ref</option>

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131 <option value="sumaclust">sumaclust</option>

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132 <option value="swarm">swarm</option>

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133 </param>

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134 <when value="uclust_ref">

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135 <param default="/home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta"

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136 label="-r/--refseqs_fp: Path to reference sequences to search

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137 against when using -m uclust_ref, -m usearch_ref [default:

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138 /home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta]" name="refseqs_fp" optional="True" type="data"/>

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139 <param default="0.97" label="-s/--similarity: Sequence similarity

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140 threshold (for blast, cdhit, uclust, uclust_ref, usearch,

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141 usearch_ref, usearch61, usearch61_ref, sumaclust or sortmerna

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142 [default: 0.97]" name="similarity" optional="True" type="float"/>

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143 <param label="-z/--enable_rev_strand_match: Enable reverse strand

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144 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,

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145 or usearch61_ref otu picking, will double the amount of memory

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146 used. [default: False]" name="enable_rev_strand_match"

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147 selected="False" type="boolean"/>

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148 <param label="-D/--suppress_presort_by_abundance_uclust: Suppress

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149 presorting of sequences by abundance when picking OTUs with

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150 uclust or uclust_ref [default: False]"

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151 name="suppress_presort_by_abundance_uclust" selected="False"

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152 type="boolean"/>

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153 <param label="-C/--suppress_new_clusters: Suppress creation of new

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154 clusters using seqs that don't match reference when using -m

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155 uclust_ref, -m usearch61_ref, or -m usearch_ref [default: False]"

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156 name="suppress_new_clusters" selected="False" type="boolean"/>

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157 <param default="default" label="--max_accepts: max_accepts value

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158 to uclust, uclust_ref, usearch61, and usearch61_ref. By default,

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159 will use value suggested by method (uclust: 1, usearch61: 1)

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160 [default: default]" name="max_accepts" optional="True" type="text"/>

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161 <param default="default" label="--max_rejects: max_rejects value

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162 for uclust, uclust_ref, usearch61, and usearch61_ref. With

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163 default settings, will use value recommended by clustering

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164 method used (uclust: 8, usearch61: 8 for usearch_fast_cluster

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165 option, 32 for reference and smallmem options) [default:

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166 default]" name="max_rejects" optional="True" type="text"/>

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167 <param default="8" label="--stepwords: stepwords value to uclust

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168 and uclust_ref [default: 8]" name="stepwords" optional="True"

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169 type="integer"/>

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170 </when>

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171 <when value="usearch_ref">

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172 <param default="/home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta"

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173 label="-r/--refseqs_fp: Path to reference sequences to search

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174 against when using -m blast, -m sortmerna, -m uclust_ref, -m

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175 usearch_ref, or -m usearch61_ref [default:

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176 /home12/caparmor/bioinfo/softs/sources/Qiime/qiime-1.9.0/python_modules/lib/python2.7/site-packages/qiime_default_reference-0.1.1-py2.7.egg/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta]" name="refseqs_fp" optional="True" type="data"/>

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177 <param default="0.97" label="-s/--similarity: Sequence similarity

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178 threshold (for blast, cdhit, uclust, uclust_ref, usearch,

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179 usearch_ref, usearch61, usearch61_ref, sumaclust or sortmerna

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180 [default: 0.97]" name="similarity" optional="True" type="float"/>

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181 <param label="-z/--enable_rev_strand_match: Enable reverse strand

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182 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,

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183 or usearch61_ref otu picking, will double the amount of memory

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184 used. [default: False]" name="enable_rev_strand_match" selected="False"

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185 type="boolean"/>

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186 <param label="-C/--suppress_new_clusters: Suppress creation of new

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187 clusters using seqs that don't match reference when using -m

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188 uclust_ref, -m usearch61_ref, or -m usearch_ref [default: False]"

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189 name="suppress_new_clusters" selected="False" type="boolean"/>

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190 <param default="default" label="--max_accepts: max_accepts value

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191 to uclust, uclust_ref, usearch61, and usearch61_ref. By default,

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192 will use value suggested by method (uclust: 1, usearch61: 1)

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193 [default: default]" name="max_accepts" optional="True" type="text"/>

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194 <param default="default" label="--max_rejects: max_rejects value

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195 for uclust, uclust_ref, usearch61, and usearch61_ref. With

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196 default settings, will use value recommended by clustering method

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197 used (uclust: 8, usearch61: 8 for usearch_fast_cluster option,

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198 32 for reference and smallmem options) [default: default]"

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199 name="max_rejects" optional="True" type="text"/>

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200 </when>

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201 <when value="usearch">

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202 <param default="0.97" value="0.97" label="-s/--similarity: Sequence

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203 similarity threshold (for blast, cdhit, uclust, uclust_ref,

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204 usearch, usearch_ref, usearch61, usearch61_ref, sumaclust or

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205 sortmerna [default: 0.97]" name="similarity" optional="True"

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206 type="float"/>

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207 <param label="-z/--enable_rev_strand_match: Enable reverse strand

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208 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,

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209 or usearch61_ref otu picking, will double the amount of memory

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210 used. [default: False]" name="enable_rev_strand_match"

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211 selected="False" type="boolean"/>

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212 <param default="default" label="--max_accepts: max_accepts value

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213 to uclust, uclust_ref, usearch61, and usearch61_ref. By

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214 default, will use value suggested by method (uclust: 1,

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215 usearch61: 1) [default: default]" name="max_accepts" optional="True"

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216 type="text"/>

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217 <param default="default" label="--max_rejects: max_rejects value

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218 for uclust, uclust_ref, usearch61, and usearch61_ref. With

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219 default settings, will use value recommended by clustering

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220 method used (uclust: 8, usearch61: 8 for usearch_fast_cluster

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221 option, 32 for reference and smallmem options) [default: default]"

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222 name="max_rejects" optional="True" type="text"/>

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223 <param default="0.97" value="0.97" label="-j/--percent_id_err:

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224 Percent identity threshold for cluster error detection with

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225 usearch, expressed as a fraction between 0 and 1. [default: 0.97]"

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226 name="percent_id_err" optional="True" type="float"/>

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227 <param default="2.0" label="-a/--abundance_skew: Abundance skew

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228 setting for de novo chimera detection with usearch. [default: 2.0]"

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229 name="abundance_skew" optional="True" type="float"/>

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230 <param default="None" label="-f/--db_filepath: Reference database

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231 of fasta sequences for reference based chimera detection with

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232 usearch. [default: None]" name="db_filepath" optional="True"

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233 type="data"/>

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234 <param default="0.97" value="0.97" label="--perc_id_blast: Percent

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235 ID for mapping OTUs created by usearch back to original sequence

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236 IDs [default: 0.97]" name="perc_id_blast" optional="True"

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237 type="float"/>

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238 <param label="-k/--suppress_de_novo_chimera_detection: Suppress

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239 de novo chimera detection in usearch. [default: False]"

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240 name="suppress_de_novo_chimera_detection" selected="False"

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241 type="boolean"/>

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242 <param label="--usearch_fast_cluster: Use fast clustering option

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243 for usearch or usearch61_ref with new clusters.

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244 --enable_rev_strand_match can not be enabled with this option,

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245 and the only valid option for usearch61_sort_method is 'length'.

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246 This option uses more memory than the default option for de novo

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247 clustering. [default: False]" name="usearch_fast_cluster"

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248 selected="False" type="boolean"/>

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249 </when>

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250 <when value="sumaclust">

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251 <param default="0.97" value="0.97" label="-s/--similarity: Sequence

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252 similarity threshold (for blast, cdhit, uclust, uclust_ref,

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253 usearch, usearch_ref, usearch61, usearch61_ref, sumaclust or

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254 sortmerna [default: 0.97]" name="similarity" optional="True"

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255 type="float"/>

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256 <param label="--sumaclust_exact: A sequence is assigned to the best

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257 matching seed rather than the first matching seed passing the

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258 similarity threshold [default: False]" name="sumaclust_exact"

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259 selected="False" type="boolean"/>

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260 <param default="1" label="--threads: Specify number of threads (1

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261 thread per core) to be used for usearch61, sortmerna, sumaclust and swarm commands that utilize multithreading. [default: 1]" name="threads" optional="True" type="text"/>

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262 </when>

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263 <when value="swarm">

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264 <param default="1" label="--swarm_resolution: Maximum number of

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265 differences allowed between two amplicons, meaning that two

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266 amplicons will be grouped if they have integer (or less)

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267 differences (see Swarm manual at https://github.com/torognes/swarm

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268 for more details). [default: 1]" name="swarm_resolution"

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269 optional="True" type="integer"/>

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270 <param default="1" label="--threads: Specify number of threads (1

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271 thread per core) to be used for usearch61, sortmerna, sumaclust

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272 and swarm commands that utilize multithreading. [default: 1]"

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273 name="threads" optional="True" type="text"/>

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274 </when>

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275 <when value="uclust">

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276 <param default="0.97" value="0.97" label="-s/--similarity: Sequence

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277 similarity threshold (for blast, cdhit, uclust, uclust_ref,

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278 usearch, usearch_ref, usearch61, usearch61_ref, sumaclust or

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279 sortmerna [default: 0.97]" name="similarity" optional="True"

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280 type="float"/>

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281 <param label="-z/--enable_rev_strand_match: Enable reverse strand

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282 matching for uclust, uclust_ref, usearch, usearch_ref, usearch61,

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283 or usearch61_ref otu picking, will double the amount of memory

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284 used. [default: False]" name="enable_rev_strand_match" selected="False"

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285 type="boolean"/>

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286 <param label="-A/--optimal_uclust: Pass the --optimal flag to uclust

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287 for uclust otu picking. [default: False]" name="optimal_uclust"

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288 selected="False" type="boolean"/>

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289 <param label="-D/--suppress_presort_by_abundance_uclust: Suppress

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290 presorting of sequences by abundance when picking OTUs with

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291 uclust or uclust_ref [default: False]"

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292 name="suppress_presort_by_abundance_uclust" selected="False"

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293 type="boolean"/>

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294 <param default="default" label="--max_accepts: max_accepts value

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295 to uclust, uclust_ref, usearch61, and usearch61_ref. By default,

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296 will use value suggested by method (uclust: 1, usearch61: 1)

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297 [default: default]" name="max_accepts" optional="True"

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298 type="text"/>

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299 <param default="default" label="--max_rejects: max_rejects value

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300 for uclust, uclust_ref, usearch61, and usearch61_ref. With

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301 default settings, will use value recommended by clustering

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302 method used (uclust: 8, usearch61: 8 for usearch_fast_cluster

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303 option, 32 for reference and smallmem options) [default: default]"

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304 name="max_rejects" optional="True" type="text"/>

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305 <param default="8" label="--stepwords: stepwords value to uclust

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306 and uclust_ref [default: 8]" name="stepwords" optional="True"

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307 type="integer"/>

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308 <param label="-E/--exact_uclust: Pass the --exact flag to uclust

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309 for uclust otu picking. [default: False]" name="exact_uclust"

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310 selected="False" type="boolean"/>

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311 </when>

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312 </conditional>

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313

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314 <param default="None" label="-n/--prefix_prefilter_length: Prefilter data

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315 so seqs with identical first prefix_prefilter_length are automatically

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316 grouped into a single OTU. This is useful for large sequence collections

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317 where OTU picking doesn't scale well [default: None; 100 is a good value]"

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318 name="prefix_prefilter_length" optional="True" type="integer"/>

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319 <param default="50" label="-p/--prefix_length: Prefix length when using

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320 the prefix_suffix otu picker; WARNING: CURRENTLY DIFFERENT FROM

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321 prefix_prefilter_length (-n)! [default: 50]" name="prefix_length"

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322 optional="True" type="integer"/>

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323 <param default="50" label="-u/--suffix_length: Suffix length when using

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324 the prefix_suffix otu picker [default: 50]" name="suffix_length"

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325 optional="True" type="integer"/>

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326 <param default="union" label="-F/--non_chimeras_retention: Selects subsets

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327 of sequences detected as non-chimeras to retain after de novo and

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328 reference based chimera detection. Options are intersection or union.

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329 union will retain sequences that are flagged as non-chimeric from either

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330 filter, while intersection will retain only those sequences that are

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331 flagged as non-chimeras from both detection methods. [default: union]"

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332 name="non_chimeras_retention" optional="True" type="text"/>

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333 </inputs>

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334 <outputs>

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335 <data format="txt" from_work_dir="fastasplit/*_otus.txt"

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336 name="pick_otus.txt" label="pick_otus.txt"/>

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337 <data format="txt" from_work_dir="fastasplit/*_otus.log"

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338 name="pick_otus.log" label="pick_otus.log"/>

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339 <data format="txt" from_work_dir="fastasplit/*_failures.txt"

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340 name="pick_otus_failures.txt" label="pick_otus_failures.txt"/>

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341 </outputs>

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342

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343 <tests>

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344 <test>

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345 </test>

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346 </tests>

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347

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348 <help><![CDATA[

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349 **What it does**

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350

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351 The OTU picking step assigns similar sequences to operational taxonomic units, or OTUs, by clustering sequences based on a user-defined similarity threshold. Sequences which are similar at or above the threshold level are taken to represent the presence of a taxonomic unit (e.g., a genus, when the similarity threshold is set at 0.94) in the sequence collection.

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352

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353 Currently, the following clustering methods have been implemented in QIIME:

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354

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355 1. uclust, creates "seeds" of sequences which generate clusters based on percent identity.

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356

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357 2. uclust_ref, as uclust, but takes a reference database to use as seeds. New clusters can be toggled on or off.

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358

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359 3. usearch, creates "seeds" of sequences which generate clusters based on percent identity, filters low abundance clusters, performs de novo and reference based chimera detection.

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360

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361 4. usearch_ref, as usearch, but takes a reference database to use as seeds. New clusters can be toggled on or off.

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362

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363 5. sumaclust, creates "seeds" of sequences which generate clusters based on similarity threshold.

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364

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365 6. swarm, creates "seeds" of sequences which generate clusters based on a resolution threshold.

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366

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367

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368 Chimera checking with usearch 6.X is implemented in identify_chimeric_seqs.py. Chimera checking should be done first with usearch 6.X, and the filtered resulting fasta file can then be clustered.

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369

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370

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371 The primary inputs for pick_otus.py are:

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372

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373 1. A FASTA file containing sequences to be clustered

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374

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375 2. An OTU threshold (default is 0.97, roughly corresponding to species-level OTUs);

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376

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377 3. The method to be applied for clustering sequences into OTUs.

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378

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379 pick_otus.py takes a standard fasta file as input.

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380

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381

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382 The output consists of two files (i.e. seqs_otus.txt and seqs_otus.log). The .txt file is composed of tab-delimited lines, where the first field on each line corresponds to an (arbitrary) cluster identifier, and the remaining fields correspond to sequence identifiers assigned to that cluster. Sequence identifiers correspond to those provided in the input FASTA file. Usearch (i.e. usearch quality filter) can additionally have log files for each intermediate call to usearch.

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383

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384 Example lines from the resulting .txt file:

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385

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386 = ==== ==== ====

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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387 0 seq1 seq5

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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388 1 seq2

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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389 2 seq3

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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390 3 seq4 seq6 seq7

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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391 = ==== ==== ====

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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392

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393 This result implies that four clusters were created based on 7 input sequences.

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394 The first cluster (cluster id 0) contains two sequences, sequence ids seq1 and

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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395 seq5; the second cluster (cluster id 1) contains one sequence, sequence id seq2;

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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396 the third cluster (cluster id 2) contains one sequence, sequence id seq3, and the

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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397 final cluster (cluster id 3) contains three sequences, sequence ids seq4, seq6,

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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398 and seq7.

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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399

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400 The resulting .log file contains a list of parameters passed to the pick_otus.py

c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty

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401 script along with the output location of the resulting .txt file.</help>

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402 ]]>

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403 </help>

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404

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405 <citations>

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406 <expand macro="citations" />

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407 <citation type="doi">10.1093/bioinformatics/btv231</citation>

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408 <citation type="doi">10.1093/bioinformatics/btq461</citation>

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409 <citation type="doi">10.1093/bioinformatics/bts611</citation>

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410 <citation type="doi">10.7287/peerj.preprints.386v1/supp-1</citation>

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411 </citations>

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412 </tool>

Mercurial > repos > bebatut > qiime

annotate pick_otus.xml @ 0:c1bd0c560018 draft default tip