qiime_make_otu_heatmap: generate_test

annotate generate_test_data.sh @ 2:bd379bfdaa41 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit e5d24fc90f811c8994ec8b72371ab4100d2c294c

author	iuc
date	Fri, 19 May 2017 04:08:04 -0400
parents	a3d1104d090c
children	71b9caeb675b

rev	line source
0 a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1 #!/usr/bin/env bash
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	2
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	3 # Data are from test data in https://github.com/biocore/qiime
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	4
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	5 # align_seqs
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	6 align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	7 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	8 -o 'align_seqs_pynast_uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	9 --alignment_method 'pynast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	10 --pairwise_alignment_method 'uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	11 --template_fp 'test-data/align_seqs/core_set_aligned.fasta.imputed' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	12 --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	13
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	14 align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	15 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	16 -o 'align_seqs_pynast_muscle' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	17 --alignment_method 'pynast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	18 --pairwise_alignment_method 'muscle' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	19 --min_length '50' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	20 --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	21
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	22 align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	23 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	24 -o 'align_seqs_pynast_pair_hmm' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	25 --alignment_method 'pynast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	26 --pairwise_alignment_method 'pair_hmm' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	27 --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	28
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	29 #align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	30 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	31 # -o 'align_seqs_pynast_clustal' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	32 # --alignment_method 'pynast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	33 # --pairwise_alignment_method 'clustal' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	34 # --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	35
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	36 align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	37 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	38 -o 'align_seqs_pynast_blast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	39 --alignment_method 'pynast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	40 --pairwise_alignment_method 'blast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	41 --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	42
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	43 align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	44 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	45 -o 'align_seqs_pynast_mafft' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	46 --alignment_method 'pynast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	47 --pairwise_alignment_method 'mafft' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	48 --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	49
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	50 #align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	51 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	52 # -o 'align_seqs_infernal' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	53 # --alignment_method 'infernal' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	54 # --template_fp 'test-data/align_seqs/seed.16s.reference_model.sto' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	55 # --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	56
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	57 #align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	58 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	59 # -o 'align_seqs_clustalw' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	60 # --alignment_method 'clustalw' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	61 # --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	62
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	63 align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	64 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	65 -o 'align_seqs_muscle' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	66 --alignment_method 'muscle' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	67 --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	68
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	69 align_seqs.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	70 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	71 -o 'align_seqs_mafft' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	72 --alignment_method 'mafft' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	73 --min_percent_id '0.75'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	74
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	75 #alpha_rarefaction
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	76 alpha_rarefaction.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	77 --otu_table_fp "test-data/alpha_rarefaction/otu_table.biom" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	78 --mapping_fp "test-data/alpha_rarefaction/mapping_file.txt" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	79 -o alpha_rarefaction \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	80 --num_steps '2' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	81 --tree_fp "test-data/alpha_rarefaction/rep_set.tre" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	82 --min_rare_depth '10' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	83 --max_rare_depth '50' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	84 --retain_intermediate_files
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	85 rm -rf alpha_rarefaction
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	86
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	87 # assign_taxonomy
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	88 assign_taxonomy.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	89 --input_fasta_fp 'test-data/assign_taxonomy/uclust_input_seqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	90 --assignment_method 'uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	91 --min_consensus_fraction '0.51' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	92 --similarity '0.9' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	93 --uclust_max_accepts '3' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	94 -o assign_taxonomy_uclust
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	95 cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt 'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	96 rm -rf assign_taxonomy_uclust
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	97
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	98 #assign_taxonomy.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	99 # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	100 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	101 # --assignment_method 'rdp' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	102 # --confidence '3' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	103 # -o assign_taxonomy_rdp
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	104
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	105 #assign_taxonomy.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	106 # --input_fasta_fp 'test-data/assign_taxonomy/rtax_ref_seq_set.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	107 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	108 # --assignment_method 'rtax' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	109 # --read_1_seqs_fp 'test-data/assign_taxonomy/read_1.seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	110 # --read_2_seqs_fp 'test-data/assign_taxonomy/read_2.seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	111 # --single_ok \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	112 # --no_single_ok_generic \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	113 # --read_id_regex "\S+\s+(\S+)" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	114 # --amplicon_id_regex "(\S+)\s+(\S+?)\/" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	115 # --header_id_regex "\S+\s+(\S+?)\/" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	116 # -o assign_taxonomy_rtax
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	117 #ls assign_taxonomy_rtax
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	118
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	119 #assign_taxonomy.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	120 # --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	121 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	122 # --assignment_method 'mothur' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	123 # --confidence 0.5 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	124 # -o assign_taxonomy_mothur
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	125 #ls assign_taxonomy_mothur
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	126
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	127 assign_taxonomy.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	128 --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	129 --assignment_method 'sortmerna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	130 --min_consensus_fraction "0.51" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	131 --similarity "0.9" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	132 --sortmerna_e_value "1.0" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	133 --sortmerna_coverage "0.9" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	134 --sortmerna_best_N_alignments "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	135 -o assign_taxonomy_sortmerna
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	136 cp assign_taxonomy_sortmerna/sortmerna_map.blast 'test-data/assign_taxonomy/sortmerna_map.blast'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	137 cp assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt 'test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	138 rm -rf assign_taxonomy_sortmerna
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	139
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	140 #beta_diversity
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	141 beta_diversity.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	142 --input_path 'test-data/beta_diversity/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	143 -o beta_diversity_1 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	144 --metrics 'unweighted_unifrac,weighted_unifrac' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	145 --tree_path 'test-data/beta_diversity/rep_set.tre'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	146 md5 'beta_diversity_1/unweighted_unifrac_otu_table.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	147 md5 'beta_diversity_1/weighted_unifrac_otu_table.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	148 rm -rf beta_diversity_1
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	149
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	150 beta_diversity.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	151 --input_path 'test-data/beta_diversity/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	152 -o beta_diversity_2 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	153 --metrics 'abund_jaccard,binary_chisq,binary_chord,binary_euclidean,binary_hamming,binary_jaccard,binary_lennon,binary_ochiai,binary_pearson,binary_sorensen_dice,bray_curtis,canberra,chisq,chord,euclidean,gower,hellinger,kulczynski,manhattan,morisita_horn,pearson,soergel,spearman_approx,specprof,unifrac_g,unifrac_g_full_tree,unweighted_unifrac,unweighted_unifrac_full_tree,weighted_normalized_unifrac,weighted_unifrac' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	154 --tree_path 'test-data/beta_diversity/rep_set.tre'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	155 md5 'beta_diversity_2/canberra_otu_table.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	156 md5 'beta_diversity_2/pearson_otu_table.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	157 rm -rf beta_diversity_2
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	158
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	159 #beta_diversity_through_plots
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	160 beta_diversity_through_plots.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	161 --otu_table_fp 'test-data/beta_diversity_through_plots/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	162 --mapping_fp 'test-data/beta_diversity_through_plots/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	163 --output_dir beta_diversity_through_plots \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	164 --tree_fp 'test-data/beta_diversity_through_plots/rep_set.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	165 --parallel
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	166 cp beta_diversity_through_plots/unweighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	167 cp beta_diversity_through_plots/unweighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	168 cp beta_diversity_through_plots/weighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	169 cp beta_diversity_through_plots/weighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	170 rm -rf beta_diversity_through_plots
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	171
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	172 # compare_categories
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	173 compare_categories.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	174 --method 'adonis' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	175 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	176 --mapping_file 'test-data/compare_categories/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	177 --categories 'Treatment' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	178 -o compare_categories_1 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	179 --num_permutations '999'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	180 cp compare_categories_1/adonis_results.txt "test-data/compare_categories/adonis_results.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	181 rm -rf compare_categories_1
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	182
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	183 compare_categories.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	184 --method 'dbrda' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	185 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	186 --mapping_file 'test-data/compare_categories/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	187 --categories 'Treatment' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	188 -o compare_categories_2 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	189 --num_permutations '99'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	190 cp compare_categories_2/* "test-data/compare_categories/"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	191 rm -rf compare_categories_2
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	192
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	193 # core_diversity_analyses
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	194 core_diversity_analyses.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	195 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	196 -o core_diversity_analyses_1 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	197 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	198 --sampling_depth 22 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	199 --tree_fp 'test-data/core_diversity_analyses/rep_set.tre'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	200 cp core_diversity_analyses_1/bdiv_even22/unweighted_unifrac_pc.txt 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	201 rm -rf core_diversity_analyses_1
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	202
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	203 core_diversity_analyses.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	204 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	205 -o core_diversity_analyses_2 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	206 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	207 --sampling_depth 22 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	208 --nonphylogenetic_diversity \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	209 --suppress_taxa_summary \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	210 --suppress_beta_diversity \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	211 --suppress_alpha_diversity \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	212 --suppress_group_significance
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	213 rm -rf core_diversity_analyses_2
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	214
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	215 # filter_alignment
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	216 filter_alignment.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	217 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	218 -o 'filter_alignment_default' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	219 --allowed_gap_frac '0.999999' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	220 --threshold '3.0'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	221
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	222 filter_alignment.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	223 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	224 -o 'filter_alignment_without_mask_filter_and_outliers' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	225 --suppress_lane_mask_filter \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	226 --allowed_gap_frac '0.999999' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	227 --remove_outliers \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	228 --threshold '3.0'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	229
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	230 filter_alignment.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	231 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	232 -o 'filter_alignment_entropy' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	233 --allowed_gap_frac '0.999999' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	234 --threshold '3.0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	235 --entropy_threshold '0.1'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	236
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	237 # filter_fasta
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	238 filter_fasta.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	239 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	240 --output_fasta_fp 'filter_fasta_otu_map.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	241 --otu_map 'test-data/filter_fasta/otu_map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	242
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	243 filter_fasta.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	244 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	245 --output_fasta_fp 'filter_fasta_otu_map_negate.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	246 --otu_map 'test-data/filter_fasta/otu_map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	247 --negate
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	248
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	249 filter_fasta.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	250 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	251 --output_fasta_fp 'filter_fasta_seq_id.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	252 --seq_id_fp 'test-data/filter_fasta/seqs_to_keep.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	253
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	254 filter_fasta.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	255 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	256 --output_fasta_fp 'filter_fasta_otu_table.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	257 --biom_fp 'test-data/filter_fasta/otu_table.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	258
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	259 filter_fasta.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	260 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	261 --output_fasta_fp 'filter_fasta_subject_fasta.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	262 --subject_fasta_fp 'test-data/filter_fasta/sl_inseqs.fasta'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	263
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	264 filter_fasta.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	265 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	266 --output_fasta_fp 'filter_fasta_seq_id_prefix.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	267 --seq_id_prefix 'S5'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	268
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	269 filter_fasta.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	270 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	271 --output_fasta_fp 'filter_fasta_sample_id.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	272 --sample_id_fp 'test-data/filter_fasta/map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	273
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	274 # filter_otus_from_otu_table
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	275 filter_otus_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	276 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	277 --min_count '2' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	278 --max_count '1000' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	279 --min_samples '5' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	280 --max_samples '350' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	281 --output_fp 'test-data/filter_otus_from_otu_table/filtered_otu_table.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	282
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	283 filter_otus_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	284 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	285 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	286 --output_fp 'test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	287
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	288 filter_otus_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	289 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	290 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	291 --negate_ids_to_exclude \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	292 --output_fp 'test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	293
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	294 # filter_samples_from_otu_table
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	295 filter_samples_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	296 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	297 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	298 --min_count '150'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	299 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	300 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	301 -o 'test-data/filter_samples_from_otu_table/abundance_min.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	302 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	303 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	304
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	305 filter_samples_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	306 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	307 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	308 --min_count '0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	309 --max_count '149'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	310 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	311 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	312 -o 'test-data/filter_samples_from_otu_table/abundance_max.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	313 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	314 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	315
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	316 filter_samples_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	317 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	318 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	319 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	320 --output_mapping_fp 'test-data/filter_samples_from_otu_table/metadata_positive.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	321 -s 'Treatment:Control'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	322 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	323 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	324 -o 'test-data/filter_samples_from_otu_table/metadata_positive.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	325 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	326 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	327
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	328 filter_samples_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	329 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	330 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	331 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	332 -s 'Treatment:*,!Control'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	333 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	334 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	335 -o 'test-data/filter_samples_from_otu_table/metadata_negative.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	336 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	337 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	338
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	339 filter_samples_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	340 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	341 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	342 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	343 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	344 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	345 -o 'test-data/filter_samples_from_otu_table/id_positive.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	346 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	347 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	348
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	349 filter_samples_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	350 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	351 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	352 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	353 --negate_sample_id_fp
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	354 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	355 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	356 -o 'test-data/filter_samples_from_otu_table/id_negative.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	357 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	358 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	359
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	360 # filter_taxa_from_otu_table
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	361 filter_taxa_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	362 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	363 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	364 --positive_taxa 'p__Bacteroidetes,p__Firmicutes' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	365 --metadata_field 'taxonomy'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	366 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	367 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	368 -o 'test-data/filter_taxa_from_otu_table/positive_taxa.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	369 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	370 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	371
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	372 filter_taxa_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	373 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	374 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	375 --negative_taxa 'p__Bacteroidetes,p__Firmicutes' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	376 --metadata_field 'taxonomy'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	377 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	378 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	379 -o 'test-data/filter_taxa_from_otu_table/negative_taxa.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	380 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	381 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	382
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	383 filter_taxa_from_otu_table.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	384 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	385 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	386 --positive_taxa 'p__Firmicutes' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	387 --negative_taxa 'c__Clostridia' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	388 --metadata_field 'taxonomy'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	389 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	390 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	391 -o 'test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	392 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	393 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	394
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	395 # jackknifed_beta_diversity
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	396 jackknifed_beta_diversity.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	397 --otu_table_fp 'test-data/jackknifed_beta_diversity/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	398 --mapping_fp 'test-data/jackknifed_beta_diversity/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	399 -o jackknifed_beta_diversity \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	400 --seqs_per_sample '10' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	401 --tree_fp 'test-data/jackknifed_beta_diversity/rep_set.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	402 --master_tree 'consensus' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	403 --parallel
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	404 rm -rf jackknifed_beta_diversity
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	405
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	406 # make_emperor
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	407 cp 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' 'test-data/make_emperor/unweighted_unifrac_pc.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	408 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/make_emperor/map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	409 cp 'test-data/summarize_taxa/2_L3.txt' 'test-data/make_emperor/2_L3.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	410
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	411 make_emperor.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	412 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	413 -o make_emperor_1 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	414 --map_fp 'test-data/make_emperor/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	415 --number_of_axes '10' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	416 --add_unique_columns \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	417 --number_of_segments 8
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	418 rm -rf make_emperor_1
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	419
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	420 make_emperor.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	421 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	422 -o make_emperor_2 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	423 --map_fp 'test-data/make_emperor/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	424 --number_of_axes '10' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	425 --add_unique_columns \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	426 --number_of_segments 8 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	427 --taxa_fp 'test-data/make_emperor/2_L3.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	428 --n_taxa_to_keep 10
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	429 rm -rf make_emperor_2
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	430
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	431 # make_otu_heatmap
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	432 make_otu_heatmap.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	433 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	434 --imagetype 'pdf' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	435 --color_scheme "YlGn" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	436 --width "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	437 --height "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	438 --dpi "200" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	439 --obs_md_category "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	440 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.pdf'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	441
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	442 make_otu_heatmap.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	443 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	444 --imagetype 'png' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	445 --color_scheme "YlGn" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	446 --width "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	447 --height "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	448 --dpi "200" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	449 --obs_md_category "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	450 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.png'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	451
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	452 make_otu_heatmap.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	453 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	454 --imagetype 'svg' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	455 --color_scheme "YlGn" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	456 --width "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	457 --height "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	458 --dpi "200" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	459 --obs_md_category "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	460 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.svg'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	461
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	462 make_otu_heatmap.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	463 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	464 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	465 --imagetype 'pdf' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	466 --color_scheme "YlGn" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	467 --width "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	468 --height "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	469 --dpi "200" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	470 --obs_md_category "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	471 --output_fp 'test-data/make_otu_heatmap/sample_sorted_heatmap.pdf'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	472
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	473 make_otu_heatmap.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	474 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	475 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	476 --otu_tree 'test-data/make_otu_heatmap/rep_set.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	477 --imagetype 'pdf' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	478 --color_scheme "YlGn" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	479 --width "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	480 --height "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	481 --dpi "200" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	482 --obs_md_category "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	483 --output_fp 'test-data/make_otu_heatmap/sample_otu_sorted_heatmap.pdf'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	484
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	485 make_otu_heatmap.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	486 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	487 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	488 --category "Treatment" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	489 --imagetype 'pdf' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	490 --color_scheme "YlGn" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	491 --width "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	492 --height "5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	493 --dpi "200" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	494 --obs_md_category "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	495 --output_fp 'test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	496
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	497 # make_phylogeny
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	498 make_phylogeny.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	499 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	500 --result_fp 'test-data/make_phylogeny/fasttree_tree_method_default.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	501 --tree_method 'fasttree' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	502 --log_fp 'fasttree_tree_method_default.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	503 --root_method 'tree_method_default'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	504
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	505 make_phylogeny.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	506 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	507 --result_fp 'raxml_v730.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	508 --tree_method 'raxml_v730' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	509 --log_fp 'raxml_v730.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	510 --root_method 'tree_method_default'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	511
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	512 make_phylogeny.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	513 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	514 --result_fp 'test-data/make_phylogeny/muscle.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	515 --tree_method 'muscle' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	516 --log_fp 'muscle.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	517 --root_method 'tree_method_default'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	518
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	519 make_phylogeny.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	520 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	521 --result_fp 'test-data/make_phylogeny/clustalw.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	522 --tree_method 'clustalw' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	523 --log_fp 'clustalw.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	524 --root_method 'tree_method_default'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	525
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	526 make_phylogeny.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	527 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	528 --result_fp 'clearcut.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	529 --tree_method 'clearcut' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	530 --log_fp 'clearcut.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	531 --root_method 'tree_method_default'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	532
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	533 make_phylogeny.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	534 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	535 --result_fp 'test-data/make_phylogeny/fasttree_midpoint.tre' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	536 --tree_method 'fasttree' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	537 --log_fp 'fasttree_midpoint.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	538 --root_method 'midpoint'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	539
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	540 # multiple_join_paired_ends
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	541 multiple_join_paired_ends.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	542 --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	543 --output_dir 'test-data/multiple_join_paired_ends/output_without_barcode' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	544 --read1_indicator 'forward_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	545 --read2_indicator 'reverse_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	546 --leading_text '' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	547 --trailing_text ''
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	548
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	549 #multiple_join_paired_ends.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	550 # --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	551 # --output_dir 'multiple_join_paired_ends_without_barcode_parameter_files' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	552 # --parameter_fp 'test-data/multiple_join_paired_ends/qiime_parameters.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	553 # --read1_indicator '_R1_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	554 # --read2_indicator '_R2_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	555 # --leading_text '' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	556 # --trailing_text ''
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	557
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	558 multiple_join_paired_ends.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	559 --input_dir 'test-data/multiple_join_paired_ends/with_barcode/' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	560 --output_dir 'test-data/multiple_join_paired_ends/output_with_barcode' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	561 --read1_indicator 'forward_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	562 --read2_indicator 'reverse_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	563 --match_barcodes \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	564 --barcode_indicator 'barcode_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	565 --leading_text '' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	566 --trailing_text ''
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	567
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	568 # multiple_split_libraries_fastq
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	569 multiple_split_libraries_fastq.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	570 --input_dir 'test-data/multiple_split_libraries_fastq/input' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	571 --output_dir 'multiple_split_libraries_fastq' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	572 --demultiplexing_method 'mapping_barcode_files' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	573 --read_indicator 'reads_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	574 --barcode_indicator 'barcodes_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	575 --mapping_indicator 'mapping_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	576 --mapping_extensions 'txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	577 --leading_text '' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	578 --trailing_text '' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	579 --sampleid_indicator '.'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	580
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	581 multiple_split_libraries_fastq.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	582 --input_dir 'test-data/multiple_split_libraries_fastq/input' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	583 --output_dir 'multiple_split_libraries_fastq_with_parameter_file' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	584 --demultiplexing_method 'mapping_barcode_files' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	585 --parameter_fp 'test-data/multiple_split_libraries_fastq/qiime_parameters.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	586 --read_indicator 'reads_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	587 --barcode_indicator 'barcodes_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	588 --mapping_indicator 'mapping_' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	589 --mapping_extensions 'txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	590 --leading_text '' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	591 --trailing_text '' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	592 --sampleid_indicator '.'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	593
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	594 # pick_closed_reference_otus
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	595 pick_closed_reference_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	596 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	597 --output_dir 'pick_closed_reference_otus' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	598 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	599 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	600 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	601 -i 'pick_closed_reference_otus/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	602 -o 'test-data/pick_closed_reference_otus/basic_otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	603 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	604
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	605 pick_closed_reference_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	606 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	607 --output_dir 'pick_closed_reference_otus_sortmerna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	608 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	609 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	610 --parameter_fp 'test-data/pick_closed_reference_otus/sortmerna_params.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	611 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	612 -i 'pick_closed_reference_otus_sortmerna/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	613 -o 'test-data/pick_closed_reference_otus/sortmerna_otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	614 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	615
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	616 pick_closed_reference_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	617 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	618 --output_dir 'pick_closed_reference_otus_assign_taxonomy' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	619 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	620 --assign_taxonomy
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	621 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	622 -i 'pick_closed_reference_otus_assign_taxonomy/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	623 -o 'test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	624 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	625
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	626 pick_closed_reference_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	627 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	628 --output_dir 'pick_closed_reference_otus_suppress_taxonomy_assignment' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	629 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	630 --suppress_taxonomy_assignment
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	631 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	632 -i 'pick_closed_reference_otus_suppress_taxonomy_assignment/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	633 -o 'test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	634 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	635
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	636 # pick_open_reference_otus
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	637 pick_open_reference_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	638 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	639 -o pick_open_reference_otus_1 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	640 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	641 --otu_picking_method 'uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	642 --new_ref_set_id 'New' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	643 --parallel \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	644 --percent_subsample '0.001' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	645 --prefilter_percent_id '0.0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	646 --minimum_failure_threshold '100000' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	647 --min_otu_size '2'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	648 cp pick_open_reference_otus_1/final_otu_map.txt 'test-data/pick_open_reference_otus/1_final_otu_map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	649 cp pick_open_reference_otus_1/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/1_final_otu_map_mc.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	650 cp pick_open_reference_otus_1/rep_set.tre 'test-data/pick_open_reference_otus/1_rep_set_tree.tre'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	651 rm -rf pick_open_reference_otus_1
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	652
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	653 pick_open_reference_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	654 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	655 -o pick_open_reference_otus_2 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	656 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	657 --otu_picking_method 'uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	658 --new_ref_set_id 'New' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	659 --parallel \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	660 --percent_subsample '0.001' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	661 --prefilter_percent_id '0.0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	662 --minimum_failure_threshold '100000' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	663 --min_otu_size '3' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	664 --suppress_taxonomy_assignment \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	665 --suppress_align_and_tree
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	666 cp pick_open_reference_otus_2/final_otu_map.txt 'test-data/pick_open_reference_otus/2_final_otu_map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	667 cp pick_open_reference_otus_2/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/2_final_otu_map_mc.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	668 rm -rf pick_open_reference_otus_2
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	669
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	670 pick_open_reference_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	671 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	672 -o pick_open_reference_otus_3 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	673 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	674 --otu_picking_method 'uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	675 --new_ref_set_id 'New' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	676 --parallel \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	677 --percent_subsample '0.001' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	678 --prefilter_percent_id '0.0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	679 --minimum_failure_threshold '100000' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	680 --min_otu_size '10' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	681 --suppress_taxonomy_assignment
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	682 cp pick_open_reference_otus_3/final_otu_map.txt 'test-data/pick_open_reference_otus/3_final_otu_map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	683 cp pick_open_reference_otus_3/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/3_final_otu_map_mc.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	684 cp pick_open_reference_otus_3/rep_set.tre 'test-data/pick_open_reference_otus/3_rep_set_tree.tre'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	685 rm -rf pick_open_reference_otus_3
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	686
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	687 # pick_otus
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	688 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	689 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	690 -o 'pick_otus_uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	691 --otu_picking_method 'uclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	692 --similarity "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	693 --denovo_otu_id_prefix "denovo" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	694 --max_accepts "1" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	695 --max_rejects "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	696 --stepwords "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	697 --word_length "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	698 --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	699
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	700 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	701 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	702 -o 'pick_otus_sortmerna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	703 --otu_picking_method "sortmerna" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	704 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	705 --sortmerna_e_value "1" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	706 --sortmerna_coverage "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	707 --sortmerna_tabular \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	708 --sortmerna_best_N_alignments "1" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	709 --sortmerna_max_pos "10000" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	710 --similarity "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	711 --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	712
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	713 #pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	714 # -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	715 # -o 'pick_otus_mothur' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	716 # --otu_picking_method "mothur" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	717 # --clustering_algorithm "furthest" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	718 # --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	719
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	720 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	721 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	722 -o 'pick_otus_trie' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	723 --otu_picking_method "trie" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	724 --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	725
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	726 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	727 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	728 -o 'pick_otus_uclust_ref' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	729 --otu_picking_method "uclust_ref" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	730 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	731 --similarity "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	732 --max_accepts "1" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	733 --max_rejects "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	734 --stepwords "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	735 --word_length "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	736 --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	737
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	738 #pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	739 # -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	740 # -o 'pick_otus_blast' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	741 # --otu_picking_method "blast" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	742 # --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	743 # --similarity "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	744 # --max_e_value_blast "1e-10" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	745 # --min_aligned_percent "0.5" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	746 # --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	747
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	748 # pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	749 # -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	750 # -o 'pick_otus_sumaclust' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	751 # --otu_picking_method "sumaclust" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	752 # --similarity "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	753 # --sumaclust_l \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	754 # --denovo_otu_id_prefix "denovo" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	755 # --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	756
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	757 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	758 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	759 -o 'pick_otus_swarm' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	760 --otu_picking_method "swarm" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	761 --denovo_otu_id_prefix "denovo" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	762 --swarm_resolution "1" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	763 --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	764
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	765 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	766 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	767 -o 'pick_otus_prefix_suffix' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	768 --otu_picking_method "prefix_suffix" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	769 --prefix_length "50" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	770 --suffix_length "50" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	771 --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	772
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	773 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	774 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	775 -o 'pick_otus_cdhit' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	776 --otu_picking_method "cdhit" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	777 --similarity "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	778 --non_chimeras_retention "union"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	779
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	780 pick_otus.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	781 -i 'test-data/pick_otus/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	782 -o 'pick_otus_uclust_intersection' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	783 --otu_picking_method "uclust" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	784 --similarity "0.97" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	785 --denovo_otu_id_prefix "denovo" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	786 --max_accepts "1" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	787 --max_rejects "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	788 --stepwords "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	789 --word_length "8" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	790 --non_chimeras_retention "intersection"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	791
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	792 # pick_rep_set
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	793 pick_rep_set.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	794 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	795 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	796 --rep_set_picking_method 'first' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	797 --sort_by 'otu' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	798 --result_fp 'test-data/pick_rep_set/first_otu_fasta.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	799 --log_fp 'test-data/pick_rep_set/first_otu_fasta.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	800
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	801 pick_rep_set.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	802 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	803 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	804 --reference_seqs_fp 'test-data/pick_rep_set/refseqs.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	805 --rep_set_picking_method 'first' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	806 --sort_by 'otu' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	807 --result_fp 'test-data/pick_rep_set/first_otu_fasta_ref.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	808 --log_fp 'test-data/pick_rep_set/first_otu_fasta_ref.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	809
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	810 pick_rep_set.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	811 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	812 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	813 --rep_set_picking_method 'longest' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	814 --sort_by 'otu' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	815 --result_fp 'test-data/pick_rep_set/longest_otu_fasta.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	816 --log_fp 'test-data/pick_rep_set/longest_otu_fasta.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	817
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	818 pick_rep_set.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	819 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	820 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	821 --rep_set_picking_method 'most_abundant' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	822 --sort_by 'otu' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	823 --result_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	824 --log_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	825
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	826 pick_rep_set.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	827 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	828 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	829 --rep_set_picking_method 'random' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	830 --sort_by 'otu' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	831 --result_fp 'test-data/pick_rep_set/random_otu_fasta.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	832 --log_fp 'test-data/pick_rep_set/random_otu_fasta.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	833
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	834 pick_rep_set.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	835 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	836 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	837 --rep_set_picking_method 'first' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	838 --sort_by 'seq_id' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	839 --result_fp 'test-data/pick_rep_set/first_seq_id_fasta.fasta' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	840 --log_fp 'test-data/pick_rep_set/first_seq_id_fasta.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	841
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	842 # plot_taxa_summary
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	843 plot_taxa_summary.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	844 --counts_fname 'test-data/plot_taxa_summary/phylum.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	845 --dir_path 'test-data/plot_taxa_summary/phylum' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	846 --labels 'phylum' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	847 --num_categories '20' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	848 --background_color 'white' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	849 --dpi '80' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	850 --x_width '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	851 --y_height '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	852 --bar_width '0.75' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	853 --type_of_file 'png' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	854 --chart_type 'area,bar,pie' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	855 --resize_nth_label '0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	856 --label_type 'categorical'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	857
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	858 plot_taxa_summary.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	859 --counts_fname 'test-data/plot_taxa_summary/phylum.txt,test-data/plot_taxa_summary/class.txt,test-data/plot_taxa_summary/genus.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	860 --dir_path 'test-data/plot_taxa_summary/phylum_class_genus' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	861 --labels 'Phylum,Class,Genus' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	862 --num_categories '20' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	863 --background_color 'white' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	864 --dpi '80' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	865 --x_width '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	866 --y_height '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	867 --bar_width '0.75' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	868 --type_of_file 'png' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	869 --chart_type 'area,bar,pie' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	870 --resize_nth_label '0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	871 --label_type 'categorical'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	872
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	873 plot_taxa_summary.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	874 --counts_fname 'test-data/plot_taxa_summary/class.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	875 --dir_path 'test-data/plot_taxa_summary/class' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	876 --labels 'Class' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	877 --num_categories '10' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	878 --background_color 'white' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	879 --dpi '80' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	880 --x_width '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	881 --y_height '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	882 --bar_width '0.75' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	883 --chart_type 'pie' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	884 --type_of_file 'svg' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	885 --include_html_legend \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	886 --resize_nth_label '0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	887 --label_type 'categorical'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	888
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	889 plot_taxa_summary.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	890 --counts_fname 'test-data/plot_taxa_summary/class.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	891 --dir_path 'test-data/plot_taxa_summary/class_colorby' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	892 --labels 'Class' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	893 --num_categories '20' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	894 --colorby 'PC.636,PC.635' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	895 --background_color 'white' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	896 --dpi '80' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	897 --x_width '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	898 --y_height '12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	899 --bar_width '0.75' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	900 --type_of_file 'pdf' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	901 --chart_type 'area,bar,pie' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	902 --resize_nth_label '0' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	903 --label_type 'categorical'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	904
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	905 # split_libraries
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	906 split_libraries.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	907 --map 'test-data/split_libraries/mapping_file.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	908 -o split_libraries \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	909 --fasta 'test-data/split_libraries/reads_1.fna,test-data/split_libraries/reads_2.fna' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	910 --qual 'test-data/split_libraries/reads_1.qual,test-data/split_libraries/reads_2.qual' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	911 --min_qual_score 25 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	912 --qual_score_window 0 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	913 --record_qual_scores \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	914 --min_seq_length 200 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	915 --max_seq_length 1000 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	916 --max_ambig 6 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	917 --max_homopolymer 6 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	918 --max_primer_mismatch 0 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	919 --barcode_type 'golay_12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	920 --max_barcode_errors 1.5 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	921 --start_numbering_at 1
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	922 cp split_libraries/seqs.fna 'test-data/split_libraries/seqs.fna'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	923 cp split_libraries/split_library_log.txt 'test-data/split_libraries/split_library_log'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	924 cp split_libraries/histograms.txt 'test-data/split_libraries/histograms.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	925 cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	926 rm -rf split_libraries
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	927
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	928 # split_libraries_fastq
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	929 split_libraries_fastq.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	930 --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	931 -o split_libraries \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	932 --mapping_fps 'test-data/map.tsv' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	933 --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	934 --store_qual_scores \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	935 --store_demultiplexed_fastq \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	936 --max_bad_run_length 3 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	937 --min_per_read_length_fraction 0.75 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	938 --sequence_max_n 0 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	939 --start_seq_id 0 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	940 --barcode_type 'golay_12' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	941 --max_barcode_errors 1.5
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	942 cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	943 cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	944 cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	945 cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	946 rm -rf split_libraries
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	947
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	948 # summarize_taxa
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	949 cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	950 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	951
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	952 summarize_taxa.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	953 -i 'test-data/summarize_taxa/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	954 -o summarize_taxa_1 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	955 -L '2,3,4,5,6' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	956 -m 'test-data/summarize_taxa/map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	957 --md_identifier "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	958 --delimiter ";"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	959 cp summarize_taxa_1/*_L2.txt "test-data/summarize_taxa/1_L2.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	960 cp summarize_taxa_1/*_L3.txt "test-data/summarize_taxa/1_L3.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	961 cp summarize_taxa_1/*_L4.txt "test-data/summarize_taxa/1_L4.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	962 cp summarize_taxa_1/*_L5.txt "test-data/summarize_taxa/1_L5.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	963 cp summarize_taxa_1/*_L6.txt "test-data/summarize_taxa/1_L6.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	964 rm -rf summarize_taxa_1
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	965
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	966 summarize_taxa.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	967 -i 'test-data/summarize_taxa/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	968 -o summarize_taxa_2 \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	969 -L '3,6' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	970 --md_identifier "taxonomy" \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	971 --delimiter ";"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	972 cp summarize_taxa_2/*_L3.txt "test-data/summarize_taxa/2_L3.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	973 cp summarize_taxa_2/*_L6.txt "test-data/summarize_taxa/2_L6.txt"
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	974 rm -rf summarize_taxa_2
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	975
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	976 # summarize_taxa_through_plots
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	977 summarize_taxa_through_plots.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	978 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	979 --output_dir summarize_taxa_through_plots_mapping \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	980 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	981 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	982 -i 'summarize_taxa_through_plots_mapping/otu_table_L2.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	983 -o 'summarize_taxa_through_plots_mapping/otu_table_L2_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	984 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	985 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	986 -i 'summarize_taxa_through_plots_mapping/otu_table_L3.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	987 -o 'summarize_taxa_through_plots_mapping/otu_table_L3_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	988 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	989 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	990 -i 'summarize_taxa_through_plots_mapping/otu_table_L4.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	991 -o 'summarize_taxa_through_plots_mapping/otu_table_L4_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	992 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	993 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	994 -i 'summarize_taxa_through_plots_mapping/otu_table_L5.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	995 -o 'summarize_taxa_through_plots_mapping/otu_table_L5_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	996 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	997 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	998 -i 'summarize_taxa_through_plots_mapping/otu_table_L6.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	999 -o 'summarize_taxa_through_plots_mapping/otu_table_L6_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1000 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1001 cp summarize_taxa_through_plots_mapping/*.txt test-data/summarize_taxa_through_plots/mapping/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1002 cp summarize_taxa_through_plots_mapping/*_json.biom test-data/summarize_taxa_through_plots/mapping/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1003 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping/area_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1004 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping/bar_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1005
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1006 summarize_taxa_through_plots.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1007 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1008 --output_dir summarize_taxa_through_plots_mapping_categories \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1009 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1010 --mapping_category 'Treatment'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1011 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1012 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1013 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1014 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1015 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1016 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1017 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1018 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1019 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1020 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1021 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1022 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1023 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1024 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1025 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1026 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1027 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1028 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1029 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1030 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1031 cp summarize_taxa_through_plots_mapping_categories/*.txt test-data/summarize_taxa_through_plots/mapping_categories/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1032 cp summarize_taxa_through_plots_mapping_categories/*_json.biom test-data/summarize_taxa_through_plots/mapping_categories/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1033 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1034 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1035
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1036 summarize_taxa_through_plots.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1037 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1038 --output_dir summarize_taxa_through_plots_mapping_sort \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1039 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1040 --sort
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1041 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1042 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1043 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1044 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1045 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1046 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1047 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1048 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1049 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1050 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1051 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1052 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1053 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1054 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1055 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1056 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1057 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1058 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1059 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1060 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1061 cp summarize_taxa_through_plots_mapping_sort/*.txt test-data/summarize_taxa_through_plots/mapping_sort/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1062 cp summarize_taxa_through_plots_mapping_sort/*_json.biom test-data/summarize_taxa_through_plots/mapping_sort/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1063 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1064 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1065
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1066 summarize_taxa_through_plots.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1067 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1068 --output_dir summarize_taxa_through_plots_without_mapping
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1069 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1070 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L2.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1071 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L2_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1072 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1073 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1074 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L3.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1075 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L3_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1076 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1077 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1078 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L4.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1079 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L4_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1080 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1081 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1082 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L5.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1083 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L5_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1084 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1085 biom convert \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1086 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L6.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1087 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L6_json.biom' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1088 --to-json
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1089 cp summarize_taxa_through_plots_without_mapping/*.txt test-data/summarize_taxa_through_plots/without_mapping/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1090 cp summarize_taxa_through_plots_without_mapping/*_json.biom test-data/summarize_taxa_through_plots/without_mapping/
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1091 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/area_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1092 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1093
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1094 # upgma_cluster
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1095 upgma_cluster.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1096 --input_path 'test-data/upgma_cluster/' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1097 --output_path 'test-data/upgma_cluster/'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1098
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1099 # validate_mapping_file
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1100 validate_mapping_file.py \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1101 -m 'test-data/validate_mapping_file/map.tsv' \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1102 -o validate_mapping_file_output \
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1103 -c '_'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1104 cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1105 cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1106 cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt'
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1107 rm -rf validate_mapping_file_output
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1108
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1109
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1110
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1111
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1112
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1113
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1114
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1115
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1116
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1117
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1118
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1119
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1120
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1121
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1122
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1123
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1124
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1125
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862 iuc parents: diff changeset	1126

Mercurial > repos > iuc > qiime_make_otu_heatmap

annotate generate_test_data.sh @ 2:bd379bfdaa41 draft