qiime_pick_otus: pick_otus.xml annotate

annotate pick_otus.xml @ 7:241c55a65e1f draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"

author	iuc
date	Thu, 05 Dec 2019 07:47:04 -0500
parents	127947ced93f
children

rev	line source
7 241c55a65e1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c" iuc parents: 5 diff changeset	1 <tool id="qiime_pick_otus" name="Perform OTU picking" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
5 127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	2 <description> (pick_otus)</description>
0 f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	3 <macros>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	4 <import>macros.xml</import>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	5 </macros>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	6 <expand macro="requirements">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	7 <requirement type="package" version="2.1b">sortmerna</requirement>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	8 <!--<requirement type="package" version="1.38.1.1">mothur</requirement>-->
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	9 <!--<requirement type="package" version="2.2.22">blast-legacy</requirement>-->
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	10 <requirement type="package" version="4.6.6">cd-hit</requirement>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	11 </expand>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	12 <version_command>pick_otus.py --version</version_command>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	13 <command detect_errors="aggressive"><![CDATA[
5 127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	14 pick_otus.py
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	15 --input_seqs_filepath '$input_seqs_filepath'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	16 --output_dir pick_otus
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	17 --otu_picking_method '$method.otu_picking_method'
0 f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	18
5 127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	19 #if $method.otu_picking_method == "sortmerna"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	20 #if $method.references.source_selector == 'history'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	21 --refseqs_fp '$method.references.refseqs_fp'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	22 #else if $method.references.source_selector == 'cached'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	23 --refseqs_fp '$method.references.refseqs_fp.fields.path'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	24 #end if
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	25 --sortmerna_e_value '$method.sortmerna_e_value'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	26 --sortmerna_coverage '$method.sortmerna_coverage'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	27 #if $method.sortmerna_tabular.test == 'yes'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	28 --sortmerna_tabular
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	29 --sortmerna_best_N_alignments '$method.sortmerna_tabular.sortmerna_best_N_alignments'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	30 #end if
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	31 --sortmerna_max_pos '$method.sortmerna_max_pos'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	32 --similarity '$method.similarity'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	33 $method.suppress_prefilter_exact_match
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	34 --threads \${GALAXY_SLOTS:-2}
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	35 #else if $method.otu_picking_method == "mothur"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	36 --clustering_algorithm '$method.clustering_algorithm'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	37 #else if $method.otu_picking_method == "trie"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	38 $method.trie_reverse_seqs
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	39 #else if $method.otu_picking_method == "uclust_ref"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	40 #if $method.references.source_selector == 'history'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	41 --refseqs_fp '$method.references.refseqs_fp'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	42 #else if $method.references.source_selector == 'cached'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	43 --refseqs_fp '$method.references.refseqs_fp.fields.path'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	44 #end if
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	45 --similarity '$method.similarity'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	46 $method.enable_rev_strand_match
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	47 $method.suppress_presort_by_abundance_uclust
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	48 $method.suppress_new_clusters
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	49 --max_accepts '$method.max_accepts'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	50 --max_rejects '$method.max_rejects'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	51 --stepwords '$method.stepwords'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	52 --word_length '$method.word_length'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	53 #else if $method.otu_picking_method == "blast"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	54 #if $method.references.source_selector == 'history'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	55 --refseqs_fp '$method.references.refseqs_fp'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	56 #else if $method.references.source_selector == 'cached'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	57 --refseqs_fp '$method.references.refseqs_fp.fields.path'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	58 #end if
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	59 --max_e_value_blast '$method.max_e_value_blast'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	60 --min_aligned_percent '$method.min_aligned_percent'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	61 --similarity '$method.similarity'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	62 #else if $method.otu_picking_method == "sumaclust"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	63 --similarity '$method.similarity'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	64 '$method.sumaclust_exact'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	65 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	66 $method.suppress_prefilter_exact_match
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	67 --threads \${GALAXY_SLOTS:-2}
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	68 #else if $method.otu_picking_method == "swarm"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	69 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	70 --swarm_resolution '$method.swarm_resolution'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	71 --threads \${GALAXY_SLOTS:-2}
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	72 #else if $method.otu_picking_method == "prefix_suffix"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	73 --prefix_length '$method.prefix_length'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	74 --suffix_length '$method.suffix_length'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	75 #else if $method.otu_picking_method == "cdhit"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	76 --similarity '$method.similarity'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	77 #else if $method.otu_picking_method == "uclust"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	78 --similarity '$method.similarity'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	79 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	80 $method.enable_rev_strand_match
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	81 $method.suppress_presort_by_abundance_uclust
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	82 $method.optimal_uclust
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	83 $method.exact_uclust
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	84 $method.user_sort
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	85 --max_accepts '$method.max_accepts'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	86 --max_rejects '$method.max_rejects'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	87 --stepwords '$method.stepwords'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	88 --word_length '$method.word_length'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	89 $method.suppress_uclust_stable_sort
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	90 $method.suppress_prefilter_exact_match
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	91 #end if
0 f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	92
5 127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	93 #if str($prefix_prefilter_length) != ''
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	94 --prefix_prefilter_length '$prefix_prefilter_length'
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	95 #end if
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	96 $trie_prefilter
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	97 --non_chimeras_retention '$non_chimeras_retention'
0 f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	98
5 127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	99 #if $method.otu_picking_method == "sortmerna"
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	100 &&
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	101 rm pick_otus/sortmerna_otus.log
127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	102 #end if
0 f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	103 ]]></command>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	104 <inputs>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	105 <param argument="--input_seqs_filepath" type="data" format="fasta" label="Input sequences file"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	106 <conditional name="method">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	107 <param argument="--otu_picking_method" type="select" label="Method for picking OTUs">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	108 <option value="sortmerna">sortmerna</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	109 <!--<option value="mothur">mothur (requires an input file of aligned sequences)</option>-->
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	110 <option value="trie">trie</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	111 <option value="uclust_ref">uclust_ref</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	112 <!--<option value="blast">blast</option>-->
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	113 <!--<option value="sumaclust">sumaclust</option>-->
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	114 <option value="swarm">swarm</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	115 <option value="prefix_suffix">prefix_suffix</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	116 <!--<option value="cdhit">cdhit</option>-->
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	117 <option value="uclust" selected="true">uclust</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	118 </param>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	119 <when value="sortmerna">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	120 <expand macro="pick_otus_reference_source"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	121 <param argument="--sortmerna_e_value" type="float" value="1" label="Max E-value when clustering"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	122 <param argument="--sortmerna_coverage" type="float" value="0.97" min="0" max="1" label="Mininum percent query coverage (of an alignment) to consider a hit"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	123 <conditional name="sortmerna_tabular">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	124 <param argument="test" type="select" label="Output alignments in the Blast tabular format with two additional columns including the CIGAR string and the percent query coverage?">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	125 <option value="yes">Yes</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	126 <option value="no" selected="true">No</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	127 </param>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	128 <when value="yes">
5 127947ced93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380 iuc parents: 0 diff changeset	129 <param argument="--sortmerna_best_N_alignments" type="integer" value="1" label="How many alignments per read will be written"/>
0 f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	130 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	131 <when value="no"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	132 </conditional>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	133 <param argument="--sortmerna_max_pos" type="integer" value="10000" label="Maximum number of positions per seed to store in the indexed database"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	134 <expand macro="pick_otus_similarity"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	135 <expand macro="pick_otus_suppress_prefilter_exact_match"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	136 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	137 <when value="mothur">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	138 <param argument="--clustering_algorithm" type="select" label="Clustering algorithm">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	139 <option value="furthest" selected="true">furthest</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	140 <option value="nearest">nearest</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	141 <option value="average">average</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	142 </param>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	143 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	144 <when value="trie">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	145 <param argument="--trie_reverse_seqs" type="boolean" truevalue="--trie_reverse_seqs" falsevalue="" checked="false" label="Reverse seqs before picking OTUs for suffix (rather than prefix) collapsing?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	146 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	147 <when value="uclust_ref">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	148 <expand macro="pick_otus_reference_source"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	149 <expand macro="pick_otus_similarity"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	150 <expand macro="pick_otus_enable_rev_strand_match"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	151 <expand macro="pick_otus_suppress_presort_by_abundance_uclust"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	152 <param argument="--suppress_new_clusters" type="boolean" truevalue="--suppress_new_clusters" falsevalue="" checked="false" label="Suppress creation of new clusters using seqs that don't match reference?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	153 <expand macro="pick_otus_max"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	154 <expand macro="pick_otus_stepwords"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	155 <expand macro="pick_otus_word_length"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	156 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	157 <when value="blast">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	158 <expand macro="pick_otus_reference_source"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	159 <expand macro="pick_otus_similarity"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	160 <param argument="--max_e_value_blast" type="float" value="1e-10" label="Max E-value when clustering"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	161 <param argument="--min_aligned_percent" type="float" value="0.5" min="0" max="1" label="Minimum percent of query sequence that can be aligned to consider a hit"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	162 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	163 <when value="sumaclust">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	164 <expand macro="pick_otus_similarity"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	165 <param argument="--sumaclust_exact" type="boolean" truevalue="--sumaclust_exact" falsevalue="" checked="false" label="Assign a sequence to the best matching seed rather than the first matching seed passing the similarity threshold?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	166 <param argument="--sumaclust_l" type="boolean" truevalue="--sumaclust_l" falsevalue="" checked="true" label="Reference sequence length if the shortest?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	167 <expand macro="pick_otus_denovo_otu_id_prefix"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	168 <expand macro="pick_otus_suppress_prefilter_exact_match"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	169 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	170 <when value="swarm">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	171 <expand macro="pick_otus_denovo_otu_id_prefix"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	172 <param argument="--swarm_resolution" type="integer" value="1" label="Maximum number of differences allowed between two amplicons" help="Two amplicons will be grouped if they have integer (or less) differences"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	173 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	174 <when value="prefix_suffix">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	175 <param argument="--prefix_length" type="integer" value="50" label="Prefix length"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	176 <param argument="--suffix_length" type="integer" value="50" label="Suffix length"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	177 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	178 <when value="cdhit">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	179 <expand macro="pick_otus_similarity"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	180 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	181 <when value="uclust">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	182 <expand macro="pick_otus_similarity"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	183 <expand macro="pick_otus_denovo_otu_id_prefix"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	184 <expand macro="pick_otus_enable_rev_strand_match"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	185 <expand macro="pick_otus_suppress_presort_by_abundance_uclust"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	186 <param argument="--optimal_uclust" type="boolean" truevalue="--optimal_uclust" falsevalue="" checked="false" label="Pass the –optimal flag to uclust?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	187 <param argument="--exact_uclust" type="boolean" truevalue="--exact_uclust" falsevalue="" checked="false" label="Pass the –exact flag to uclust?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	188 <param argument="--user_sort" type="boolean" truevalue="--user_sort" falsevalue="" checked="false" label="Pass the -user_sort flag to uclust?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	189 <expand macro="pick_otus_max"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	190 <expand macro="pick_otus_stepwords"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	191 <expand macro="pick_otus_word_length"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	192 <param argument="--suppress_uclust_stable_sort" type="boolean" truevalue="--suppress_uclust_stable_sort" falsevalue="" checked="false" label="Don't pass –stable-sort to uclust?"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	193 <expand macro="pick_otus_suppress_prefilter_exact_match"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	194 </when>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	195 </conditional>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	196 <param argument="--prefix_prefilter_length" type="integer" label="Threshold to automatically group first identical prefix_prefilter_length into a single OTU" help="This is useful for large sequence collections where OTU picking doesn't scale well" optional="true"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	197 <param argument="--trie_prefilter" type="boolean" truevalue="--trie_prefilter" falsevalue="" checked="false" label="Prefilter data so seqs which are identical prefixes of a longer seq are automatically grouped into a single OTU?" help="This is useful for large sequence collections where OTU picking doesn't scale well"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	198 <param argument="--non_chimeras_retention" type="select" label="Selects subsets of sequences detected as non-chimeras to retain after de novo and reference based chimera detection">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	199 <option value="intersection">Intersection (retains only those sequences that are flagged as non-chimeras from both detection methods)</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	200 <option value="union" selected="true">Union (retains sequences that are flagged as non-chimeric from either filter)</option>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	201 </param>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	202 </inputs>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	203 <outputs>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	204 <data name="otus" format="txt" from_work_dir="pick_otus/*_otus.txt" label="${tool.name} on ${on_string}: OTUs"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	205 <data name="log" format="txt" from_work_dir="pick_otus/*_otus.log" label="${tool.name} on ${on_string}: Log"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	206 <data name="failures" format="txt" from_work_dir="pick_otus/*_failures.txt" label="${tool.name} on ${on_string}: Failures">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	207 <filter>method['otu_picking_method'] == "sortmerna" or method['otu_picking_method'] == "uclust_ref"</filter>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	208 </data>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	209 <data name="blast_output" format="tabular" from_work_dir="pick_otus/sortmerna_otus.blast" label="${tool.name} on ${on_string}: SortMeRNA Blast output">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	210 <filter>method['otu_picking_method'] == "sortmerna" and method["sortmerna_tabular"]["test"] == "yes"</filter>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	211 </data>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	212 </outputs>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	213 <tests>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	214 <test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	215 <param name="input_seqs_filepath" value="pick_otus/seqs.fna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	216 <param name="otu_picking_method" value="uclust"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	217 <param name="similarity" value="0.97" />
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	218 <param name="denovo_otu_id_prefix" value="denovo"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	219 <param name="enable_rev_strand_match" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	220 <param name="suppress_presort_by_abundance_uclust" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	221 <param name="optimal_uclust" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	222 <param name="exact_uclust" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	223 <param name="user_sort" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	224 <param name="max_accepts" value="1"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	225 <param name="max_rejects" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	226 <param name="stepwords" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	227 <param name="word_length" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	228 <param name="suppress_uclust_stable_sort" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	229 <param name="suppress_prefilter_exact_match" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	230 <param name="trie_prefilter" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	231 <param name="non_chimeras_retention" value="union"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	232 <output name="otus" md5="2ca01ee393e8a795e5d09a15c5ca77c3"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	233 <output name="log">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	234 <assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	235 <has_text text="UclustOtuPicker parameters"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	236 </assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	237 </output>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	238 </test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	239 <test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	240 <param name="input_seqs_filepath" value="pick_otus/seqs.fna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	241 <param name="otu_picking_method" value="sortmerna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	242 <param name="source_selector" value="history"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	243 <param name="refseqs_fp" value="pick_otus/refseqs.fasta"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	244 <param name="sortmerna_e_value" value="1"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	245 <param name="sortmerna_coverage" value="0.97"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	246 <param name="test" value="yes"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	247 <param name="sortmerna_best_N_alignments" value="1"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	248 <param name="sortmerna_max_pos" value="10000"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	249 <param name="similarity" value="0.97"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	250 <param name="suppress_prefilter_exact_match" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	251 <param name="trie_prefilter" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	252 <param name="non_chimeras_retention" value="union"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	253 <output name="otus" md5="dbc3e13e7da742ac3df317054821f522"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	254 <output name="log">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	255 <assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	256 <has_text text="OtuPicker parameters"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	257 <has_text text="SortMeRNA database"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	258 </assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	259 </output>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	260 <output name="failures" md5="cce9699de546618df2db9de7a8098916"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	261 <output name="blast_output" md5="214b1674f5f84dcb68c0c0c1c8a001be"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	262 </test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	263 <test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	264 <param name="input_seqs_filepath" value="pick_otus/seqs.fna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	265 <param name="otu_picking_method" value="trie"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	266 <param name="trie_reverse_seqs" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	267 <param name="trie_prefilter" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	268 <param name="non_chimeras_retention" value="union"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	269 <output name="otus" md5="441c2bc34cd6766e75585dbe2ea09f9b"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	270 <output name="log">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	271 <assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	272 <has_text text="TrieOtuPicker parameters:"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	273 </assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	274 </output>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	275 </test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	276 <test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	277 <param name="input_seqs_filepath" value="pick_otus/seqs.fna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	278 <param name="otu_picking_method" value="uclust_ref"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	279 <param name="source_selector" value="history"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	280 <param name="refseqs_fp" value="pick_otus/refseqs.fasta"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	281 <param name="similarity" value="0.97"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	282 <param name="enable_rev_strand_match" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	283 <param name="suppress_presort_by_abundance_uclust" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	284 <param name="suppress_new_clusters" value="" />
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	285 <param name="max_accepts" value="1"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	286 <param name="max_rejects" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	287 <param name="stepwords" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	288 <param name="word_length" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	289 <param name="trie_prefilter" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	290 <param name="non_chimeras_retention" value="union"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	291 <output name="otus" md5="e44b21022227e9fc213e13fd028efb81"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	292 <output name="log">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	293 <assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	294 <has_text text="OtuPicker parameters"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	295 <has_text text="Application:uclust"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	296 </assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	297 </output>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	298 <output name="failures" md5="d41d8cd98f00b204e9800998ecf8427e"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	299 </test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	300 <test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	301 <param name="input_seqs_filepath" value="pick_otus/seqs.fna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	302 <param name="otu_picking_method" value="swarm"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	303 <param name="denovo_otu_id_prefix" value="denovo"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	304 <param name="swarm_resolution" value="1"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	305 <param name="trie_prefilter" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	306 <param name="non_chimeras_retention" value="union"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	307 <output name="otus" md5="9b603183a1116071e762e31525928f94"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	308 <output name="log">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	309 <assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	310 <has_text text="OtuPicker parameters"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	311 </assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	312 </output>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	313 </test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	314 <test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	315 <param name="input_seqs_filepath" value="pick_otus/seqs.fna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	316 <param name="otu_picking_method" value="prefix_suffix"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	317 <param name="prefix_length" value="50"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	318 <param name="suffix_length" value="50"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	319 <param name="trie_prefilter" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	320 <param name="non_chimeras_retention" value="union"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	321 <output name="otus" md5="3bf79c70affb264a977fd8f2f34f2889"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	322 <output name="log">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	323 <assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	324 <has_text text="PrefixSuffixOtuPicker parameters:"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	325 </assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	326 </output>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	327 </test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	328 <test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	329 <param name="input_seqs_filepath" value="pick_otus/seqs.fna"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	330 <param name="otu_picking_method" value="uclust"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	331 <param name="similarity" value="0.97"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	332 <param name="denovo_otu_id_prefix" value="denovo"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	333 <param name="enable_rev_strand_match" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	334 <param name="suppress_presort_by_abundance_uclust" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	335 <param name="optimal_uclust" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	336 <param name="exact_uclust" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	337 <param name="user_sort" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	338 <param name="max_accepts" value="1"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	339 <param name="max_rejects" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	340 <param name="stepwords" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	341 <param name="word_length" value="8"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	342 <param name="suppress_uclust_stable_sort" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	343 <param name="suppress_prefilter_exact_match" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	344 <param name="trie_prefilter" value=""/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	345 <param name="non_chimeras_retention" value="union"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	346 <output name="otus" md5="2ca01ee393e8a795e5d09a15c5ca77c3"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	347 <output name="log">
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	348 <assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	349 <has_text text="UclustOtuPicker parameters"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	350 </assert_contents>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	351 </output>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	352 </test>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	353 </tests>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	354 <help><![CDATA[
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	355 What it does
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	356
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	357 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.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	358
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	359 Currently, the following clustering methods have been implemented in QIIME:
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	360
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	361 1. uclust, creates "seeds" of sequences which generate clusters based on percent identity.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	362
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	363 2. uclust_ref, as uclust, but takes a reference database to use as seeds. New clusters can be toggled on or off.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	364
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	365 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.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	366
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	367 4. usearch_ref, as usearch, but takes a reference database to use as seeds. New clusters can be toggled on or off.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	368
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	369 5. sumaclust, creates "seeds" of sequences which generate clusters based on similarity threshold.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	370
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	371 6. swarm, creates "seeds" of sequences which generate clusters based on a resolution threshold.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	372
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	373
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	374 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.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	375
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	376
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	377 The primary inputs for pick_otus.py are:
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	378
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	379 1. A FASTA file containing sequences to be clustered
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	380
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	381 2. An OTU threshold (default is 0.97, roughly corresponding to species-level OTUs);
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	382
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	383 3. The method to be applied for clustering sequences into OTUs.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	384
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	385 pick_otus.py takes a standard fasta file as input.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	386
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	387
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	388 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.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	389
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	390 Example lines from the resulting .txt file:
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	391
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	392 = ==== ==== ====
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	393 0 seq1 seq5
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	394 1 seq2
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	395 2 seq3
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	396 3 seq4 seq6 seq7
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	397 = ==== ==== ====
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	398
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	399 This result implies that four clusters were created based on 7 input sequences.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	400 The first cluster (cluster id 0) contains two sequences, sequence ids seq1 and
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	401 seq5; the second cluster (cluster id 1) contains one sequence, sequence id seq2;
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	402 the third cluster (cluster id 2) contains one sequence, sequence id seq3, and the
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	403 final cluster (cluster id 3) contains three sequences, sequence ids seq4, seq6,
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	404 and seq7.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	405
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	406 The resulting .log file contains a list of parameters passed to the pick_otus.py
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	407 script along with the output location of the resulting .txt file.
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	408 ]]></help>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	409 <citations>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	410 <expand macro="citations"/>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	411 <citation type="doi">10.1093/bioinformatics/btv231</citation>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	412 <citation type="doi">10.1093/bioinformatics/btq461</citation>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	413 <citation type="doi">10.1093/bioinformatics/bts611</citation>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	414 <citation type="doi">10.7287/peerj.preprints.386v1/supp-1</citation>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	415 </citations>
f77fff416ea7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	416 </tool>

Mercurial > repos > iuc > qiime_pick_otus

annotate pick_otus.xml @ 7:241c55a65e1f draft default tip