Mercurial > repos > iuc > qiime_align_seqs

annotate generate_test_data.sh @ 7:e8bb88f051ec draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
author iuc
date Thu, 05 Dec 2019 07:44:03 -0500
parents 98614f0549e3
children
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56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
1 #!/usr/bin/env bash
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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3 # Data are from test data in https://github.com/biocore/qiime
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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4
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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5 # align_seqs
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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6 align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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7 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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8 -o 'align_seqs_pynast_uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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9 --alignment_method 'pynast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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10 --pairwise_alignment_method 'uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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11 --template_fp 'test-data/align_seqs/core_set_aligned.fasta.imputed' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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12 --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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14 align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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15 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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16 -o 'align_seqs_pynast_muscle' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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17 --alignment_method 'pynast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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18 --pairwise_alignment_method 'muscle' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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19 --min_length '50' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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20 --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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22 align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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23 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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24 -o 'align_seqs_pynast_pair_hmm' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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25 --alignment_method 'pynast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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26 --pairwise_alignment_method 'pair_hmm' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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27 --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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29 #align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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30 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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31 # -o 'align_seqs_pynast_clustal' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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32 # --alignment_method 'pynast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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33 # --pairwise_alignment_method 'clustal' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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34 # --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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36 align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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37 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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38 -o 'align_seqs_pynast_blast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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39 --alignment_method 'pynast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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40 --pairwise_alignment_method 'blast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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41 --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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43 align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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44 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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45 -o 'align_seqs_pynast_mafft' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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46 --alignment_method 'pynast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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47 --pairwise_alignment_method 'mafft' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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48 --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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49
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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50 #align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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51 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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52 # -o 'align_seqs_infernal' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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53 # --alignment_method 'infernal' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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54 # --template_fp 'test-data/align_seqs/seed.16s.reference_model.sto' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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55 # --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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57 #align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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58 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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59 # -o 'align_seqs_clustalw' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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60 # --alignment_method 'clustalw' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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61 # --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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62
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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63 align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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64 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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65 -o 'align_seqs_muscle' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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66 --alignment_method 'muscle' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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67 --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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68
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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69 align_seqs.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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70 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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71 -o 'align_seqs_mafft' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72 --alignment_method 'mafft' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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73 --min_percent_id '0.75'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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74
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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75 #alpha_rarefaction
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76 alpha_rarefaction.py \
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77 --otu_table_fp "test-data/alpha_rarefaction/otu_table.biom" \
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78 --mapping_fp "test-data/alpha_rarefaction/mapping_file.txt" \
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79 -o alpha_rarefaction \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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80 --num_steps '2' \
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81 --tree_fp "test-data/alpha_rarefaction/rep_set.tre" \
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82 --min_rare_depth '10' \
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83 --max_rare_depth '50' \
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84 --retain_intermediate_files
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85 rm -rf alpha_rarefaction
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86
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87 # assign_taxonomy
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88 assign_taxonomy.py \
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89 --input_fasta_fp 'test-data/assign_taxonomy/uclust_input_seqs.fasta' \
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90 --assignment_method 'uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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91 --min_consensus_fraction '0.51' \
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92 --similarity '0.9' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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93 --uclust_max_accepts '3' \
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94 -o assign_taxonomy_uclust
3
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95 ls assign_taxonomy_uclust
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96 md5sum 'assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt'
0
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97 rm -rf assign_taxonomy_uclust
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98
3
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99 assign_taxonomy.py \
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100 --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \
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101 --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \
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102 --assignment_method 'mothur' \
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103 --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
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104 --confidence '0.5' \
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105 -o assign_taxonomy_mothur
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106 ls assign_taxonomy_mothur
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107 md5sum 'assign_taxonomy_mothur/mothur_repr_set_seqs_tax_assignments.txt'
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108 rm -rf assign_taxonomy_mothur
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109
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110 assign_taxonomy.py \
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111 --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \
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112 --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \
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113 --assignment_method 'mothur' \
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114 --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
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115 --blast_e_value '0.001' \
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116 -o assign_taxonomy_blast
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117 ls assign_taxonomy_blast
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118 md5sum 'assign_taxonomy_blast/mothur_repr_set_seqs_tax_assignments.txt'
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119 rm -rf assign_taxonomy_blast
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120
0
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121 #assign_taxonomy.py \
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122 # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \
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123 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \
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124 # --assignment_method 'rdp' \
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125 # --confidence '3' \
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126 # -o assign_taxonomy_rdp
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127
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128 #assign_taxonomy.py \
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129 # --input_fasta_fp 'test-data/assign_taxonomy/rtax_ref_seq_set.fna' \
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130 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt' \
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131 # --assignment_method 'rtax' \
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132 # --read_1_seqs_fp 'test-data/assign_taxonomy/read_1.seqs.fna' \
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133 # --read_2_seqs_fp 'test-data/assign_taxonomy/read_2.seqs.fna' \
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134 # --single_ok \
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135 # --no_single_ok_generic \
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136 # --read_id_regex "\S+\s+(\S+)" \
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137 # --amplicon_id_regex "(\S+)\s+(\S+?)\/" \
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138 # --header_id_regex "\S+\s+(\S+?)\/" \
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139 # -o assign_taxonomy_rtax
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140 #ls assign_taxonomy_rtax
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141
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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142 assign_taxonomy.py \
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143 --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
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144 --assignment_method 'sortmerna' \
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145 --min_consensus_fraction "0.51" \
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146 --similarity "0.9" \
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147 --sortmerna_e_value "1.0" \
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148 --sortmerna_coverage "0.9" \
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149 --sortmerna_best_N_alignments "5" \
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150 -o assign_taxonomy_sortmerna
3
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151 ls assign_taxonomy_sortmerna
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152 md5sum 'assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt'
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153 md5sum 'assign_taxonomy_sortmerna/sortmerna_map.blast'
0
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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154 rm -rf assign_taxonomy_sortmerna
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155
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156 #beta_diversity
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157 beta_diversity.py \
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158 --input_path 'test-data/beta_diversity/otu_table.biom' \
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159 -o beta_diversity_1 \
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160 --metrics 'unweighted_unifrac,weighted_unifrac' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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161 --tree_path 'test-data/beta_diversity/rep_set.tre'
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162 md5 'beta_diversity_1/unweighted_unifrac_otu_table.txt'
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163 md5 'beta_diversity_1/weighted_unifrac_otu_table.txt'
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164 rm -rf beta_diversity_1
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165
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166 beta_diversity.py \
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167 --input_path 'test-data/beta_diversity/otu_table.biom' \
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168 -o beta_diversity_2 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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169 --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' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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170 --tree_path 'test-data/beta_diversity/rep_set.tre'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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171 md5 'beta_diversity_2/canberra_otu_table.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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172 md5 'beta_diversity_2/pearson_otu_table.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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173 rm -rf beta_diversity_2
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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174
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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175 #beta_diversity_through_plots
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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176 beta_diversity_through_plots.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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177 --otu_table_fp 'test-data/beta_diversity_through_plots/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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178 --mapping_fp 'test-data/beta_diversity_through_plots/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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179 --output_dir beta_diversity_through_plots \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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180 --tree_fp 'test-data/beta_diversity_through_plots/rep_set.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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181 --parallel
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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182 cp beta_diversity_through_plots/unweighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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183 cp beta_diversity_through_plots/unweighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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184 cp beta_diversity_through_plots/weighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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185 cp beta_diversity_through_plots/weighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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186 rm -rf beta_diversity_through_plots
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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187
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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188 # compare_categories
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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189 compare_categories.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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190 --method 'adonis' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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191 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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192 --mapping_file 'test-data/compare_categories/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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193 --categories 'Treatment' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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194 -o compare_categories_1 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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195 --num_permutations '999'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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196 cp compare_categories_1/adonis_results.txt "test-data/compare_categories/adonis_results.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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197 rm -rf compare_categories_1
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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198
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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199 compare_categories.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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200 --method 'dbrda' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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201 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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202 --mapping_file 'test-data/compare_categories/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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203 --categories 'Treatment' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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204 -o compare_categories_2 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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205 --num_permutations '99'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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206 cp compare_categories_2/* "test-data/compare_categories/"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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207 rm -rf compare_categories_2
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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208
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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209 # core_diversity_analyses
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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210 core_diversity_analyses.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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211 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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212 -o core_diversity_analyses_1 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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213 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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214 --sampling_depth 22 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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215 --tree_fp 'test-data/core_diversity_analyses/rep_set.tre'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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216 cp core_diversity_analyses_1/bdiv_even22/unweighted_unifrac_pc.txt 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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217 rm -rf core_diversity_analyses_1
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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218
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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219 core_diversity_analyses.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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220 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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221 -o core_diversity_analyses_2 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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222 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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223 --sampling_depth 22 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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224 --nonphylogenetic_diversity \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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225 --suppress_taxa_summary \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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226 --suppress_beta_diversity \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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227 --suppress_alpha_diversity \
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228 --suppress_group_significance
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229 rm -rf core_diversity_analyses_2
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230
5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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231 # extract_barcodes
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232 extract_barcodes.py \
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233 --fastq1 'test-data/extract_barcodes/inseqs.fastq' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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234 --input_type 'barcode_single_end' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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235 -o extract_barcodes_1 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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236 --bc1_len '6' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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237 --rev_comp_bc1
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238 rm -rf extract_barcodes_1
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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239
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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240 extract_barcodes.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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241 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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242 --input_type 'barcode_paired_end' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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243 --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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244 -o extract_barcodes_2 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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245 --bc1_len '6' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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246 --bc2_len '6'
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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247 rm -rf extract_barcodes_2
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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248
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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249 extract_barcodes.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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250 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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251 --input_type 'barcode_paired_end' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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diff changeset
252 --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
253 -o extract_barcodes_3 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
254 --bc1_len '6' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
255 --bc2_len '6' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
256 --mapping_fp 'test-data/extract_barcodes/mapping_data.txt' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
257 --attempt_read_reorientation \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
258 --disable_header_match
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
259 rm -rf extract_barcodes_3
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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diff changeset
260
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
261 extract_barcodes.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
262 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
263 --input_type 'barcode_paired_stitched' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
264 -o extract_barcodes_4 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
265 --bc1_len '6' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
266 --bc2_len '8' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
267 --rev_comp_bc1 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
268 --rev_comp_bc2
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
269 rm -rf extract_barcodes_4
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
270
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
271 extract_barcodes.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
272 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
273 --input_type 'barcode_in_label' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
274 --char_delineator '#' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
275 -o extract_barcodes_5 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
276 --bc1_len '6'
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
277 rm -rf extract_barcodes_5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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diff changeset
278
0
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
279 # filter_alignment
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
280 filter_alignment.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
281 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
282 -o 'filter_alignment_default' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
283 --allowed_gap_frac '0.999999' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
284 --threshold '3.0'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
285
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
286 filter_alignment.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
287 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
288 -o 'filter_alignment_without_mask_filter_and_outliers' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
289 --suppress_lane_mask_filter \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
290 --allowed_gap_frac '0.999999' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
291 --remove_outliers \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
292 --threshold '3.0'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
293
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
294 filter_alignment.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
295 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
296 -o 'filter_alignment_entropy' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
297 --allowed_gap_frac '0.999999' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
298 --threshold '3.0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
299 --entropy_threshold '0.1'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
300
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
301 # filter_fasta
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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302 filter_fasta.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
303 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
304 --output_fasta_fp 'filter_fasta_otu_map.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
305 --otu_map 'test-data/filter_fasta/otu_map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
306
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
307 filter_fasta.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
308 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
309 --output_fasta_fp 'filter_fasta_otu_map_negate.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
310 --otu_map 'test-data/filter_fasta/otu_map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
311 --negate
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
312
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
313 filter_fasta.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
314 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
315 --output_fasta_fp 'filter_fasta_seq_id.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
316 --seq_id_fp 'test-data/filter_fasta/seqs_to_keep.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
317
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
318 filter_fasta.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
319 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
320 --output_fasta_fp 'filter_fasta_otu_table.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
321 --biom_fp 'test-data/filter_fasta/otu_table.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
322
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
323 filter_fasta.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
324 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
325 --output_fasta_fp 'filter_fasta_subject_fasta.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
326 --subject_fasta_fp 'test-data/filter_fasta/sl_inseqs.fasta'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
327
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
328 filter_fasta.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
329 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
330 --output_fasta_fp 'filter_fasta_seq_id_prefix.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
331 --seq_id_prefix 'S5'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
332
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
333 filter_fasta.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
334 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
335 --output_fasta_fp 'filter_fasta_sample_id.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
336 --sample_id_fp 'test-data/filter_fasta/map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
337
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
338 # filter_otus_from_otu_table
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
339 filter_otus_from_otu_table.py \
56adf8db7ce7 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_otus_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
341 --min_count '2' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
342 --max_count '1000' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
343 --min_samples '5' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
344 --max_samples '350' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
345 --output_fp 'test-data/filter_otus_from_otu_table/filtered_otu_table.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
346
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
347 filter_otus_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
348 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
349 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
350 --output_fp 'test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
351
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
352 filter_otus_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
353 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
354 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
355 --negate_ids_to_exclude \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
356 --output_fp 'test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
357
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
358 # filter_samples_from_otu_table
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
359 filter_samples_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
360 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
361 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
362 --min_count '150'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
363 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
364 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
365 -o 'test-data/filter_samples_from_otu_table/abundance_min.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
366 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
367 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
368
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
369 filter_samples_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
370 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
371 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
372 --min_count '0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
373 --max_count '149'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
374 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
375 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
376 -o 'test-data/filter_samples_from_otu_table/abundance_max.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
377 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
378 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
379
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
380 filter_samples_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
381 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
382 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
383 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
384 --output_mapping_fp 'test-data/filter_samples_from_otu_table/metadata_positive.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
385 -s 'Treatment:Control'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
386 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
387 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
388 -o 'test-data/filter_samples_from_otu_table/metadata_positive.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
389 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
390 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
391
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
392 filter_samples_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
393 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
394 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
395 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
396 -s 'Treatment:*,!Control'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
397 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
398 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
399 -o 'test-data/filter_samples_from_otu_table/metadata_negative.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
400 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
401 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
402
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
403 filter_samples_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
404 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
405 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
406 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
407 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
408 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
409 -o 'test-data/filter_samples_from_otu_table/id_positive.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
410 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
411 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
412
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
413 filter_samples_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
414 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
415 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
416 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
417 --negate_sample_id_fp
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
418 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
419 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
420 -o 'test-data/filter_samples_from_otu_table/id_negative.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
421 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
422 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
423
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
424 # filter_taxa_from_otu_table
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
425 filter_taxa_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
426 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
427 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
428 --positive_taxa 'p__Bacteroidetes,p__Firmicutes' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
429 --metadata_field 'taxonomy'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
430 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
431 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
432 -o 'test-data/filter_taxa_from_otu_table/positive_taxa.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
433 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
434 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
435
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
436 filter_taxa_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
437 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
438 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
439 --negative_taxa 'p__Bacteroidetes,p__Firmicutes' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
440 --metadata_field 'taxonomy'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
441 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
442 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
443 -o 'test-data/filter_taxa_from_otu_table/negative_taxa.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
444 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
445 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
446
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
447 filter_taxa_from_otu_table.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
448 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
449 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
450 --positive_taxa 'p__Firmicutes' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
451 --negative_taxa 'c__Clostridia' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
452 --metadata_field 'taxonomy'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
453 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
454 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
455 -o 'test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
456 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
457 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
458
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
459 # jackknifed_beta_diversity
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
460 jackknifed_beta_diversity.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
461 --otu_table_fp 'test-data/jackknifed_beta_diversity/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
462 --mapping_fp 'test-data/jackknifed_beta_diversity/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
463 -o jackknifed_beta_diversity \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
464 --seqs_per_sample '10' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
465 --tree_fp 'test-data/jackknifed_beta_diversity/rep_set.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
466 --master_tree 'consensus' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
467 --parallel
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
468 rm -rf jackknifed_beta_diversity
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
469
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
470 # make_emperor
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
471 cp 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' 'test-data/make_emperor/unweighted_unifrac_pc.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
472 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/make_emperor/map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
473 cp 'test-data/summarize_taxa/2_L3.txt' 'test-data/make_emperor/2_L3.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
474
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
475 make_emperor.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
476 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
477 -o make_emperor_1 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
478 --map_fp 'test-data/make_emperor/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
479 --number_of_axes '10' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
480 --add_unique_columns \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
481 --number_of_segments 8
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
482 rm -rf make_emperor_1
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
483
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
484 make_emperor.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
485 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
486 -o make_emperor_2 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
487 --map_fp 'test-data/make_emperor/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
488 --number_of_axes '10' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
489 --add_unique_columns \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
490 --number_of_segments 8 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
491 --taxa_fp 'test-data/make_emperor/2_L3.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
492 --n_taxa_to_keep 10
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
493 rm -rf make_emperor_2
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
494
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
495 # make_otu_heatmap
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
496 make_otu_heatmap.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
497 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
498 --imagetype 'pdf' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
499 --color_scheme "YlGn" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
500 --width "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
501 --height "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
502 --dpi "200" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
503 --obs_md_category "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
504 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.pdf'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
505
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
506 make_otu_heatmap.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
507 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
508 --imagetype 'png' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
509 --color_scheme "YlGn" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
510 --width "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
511 --height "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
512 --dpi "200" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
513 --obs_md_category "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
514 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.png'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
515
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
516 make_otu_heatmap.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
517 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
518 --imagetype 'svg' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
519 --color_scheme "YlGn" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
520 --width "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
521 --height "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
522 --dpi "200" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
523 --obs_md_category "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
524 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.svg'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
525
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
526 make_otu_heatmap.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
527 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
528 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
529 --imagetype 'pdf' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
530 --color_scheme "YlGn" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
531 --width "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
532 --height "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
533 --dpi "200" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
534 --obs_md_category "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
535 --output_fp 'test-data/make_otu_heatmap/sample_sorted_heatmap.pdf'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
536
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
537 make_otu_heatmap.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
538 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
539 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
540 --otu_tree 'test-data/make_otu_heatmap/rep_set.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
541 --imagetype 'pdf' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
542 --color_scheme "YlGn" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
543 --width "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
544 --height "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
545 --dpi "200" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
546 --obs_md_category "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
547 --output_fp 'test-data/make_otu_heatmap/sample_otu_sorted_heatmap.pdf'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
548
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
549 make_otu_heatmap.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
550 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
551 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
552 --category "Treatment" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
553 --imagetype 'pdf' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
554 --color_scheme "YlGn" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
555 --width "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
556 --height "5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
557 --dpi "200" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
558 --obs_md_category "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
559 --output_fp 'test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
560
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
561 # make_phylogeny
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
562 make_phylogeny.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
563 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
564 --result_fp 'test-data/make_phylogeny/fasttree_tree_method_default.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
565 --tree_method 'fasttree' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
566 --log_fp 'fasttree_tree_method_default.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
567 --root_method 'tree_method_default'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
568
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
569 make_phylogeny.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
570 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
571 --result_fp 'raxml_v730.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
572 --tree_method 'raxml_v730' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
573 --log_fp 'raxml_v730.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
574 --root_method 'tree_method_default'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
575
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
576 make_phylogeny.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
577 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
578 --result_fp 'test-data/make_phylogeny/muscle.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
579 --tree_method 'muscle' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
580 --log_fp 'muscle.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
581 --root_method 'tree_method_default'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
582
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
583 make_phylogeny.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
584 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
585 --result_fp 'test-data/make_phylogeny/clustalw.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
586 --tree_method 'clustalw' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
587 --log_fp 'clustalw.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
588 --root_method 'tree_method_default'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
589
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
590 make_phylogeny.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
591 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
592 --result_fp 'clearcut.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
593 --tree_method 'clearcut' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
594 --log_fp 'clearcut.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
595 --root_method 'tree_method_default'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
596
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
597 make_phylogeny.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
598 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
599 --result_fp 'test-data/make_phylogeny/fasttree_midpoint.tre' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
600 --tree_method 'fasttree' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
601 --log_fp 'fasttree_midpoint.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
602 --root_method 'midpoint'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
603
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
604 # multiple_join_paired_ends
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
605 multiple_join_paired_ends.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
606 --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
607 --output_dir 'test-data/multiple_join_paired_ends/output_without_barcode' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
608 --read1_indicator 'forward_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
609 --read2_indicator 'reverse_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
610 --leading_text '' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
611 --trailing_text ''
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
612
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
613 #multiple_join_paired_ends.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
614 # --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
615 # --output_dir 'multiple_join_paired_ends_without_barcode_parameter_files' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
616 # --parameter_fp 'test-data/multiple_join_paired_ends/qiime_parameters.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
617 # --read1_indicator '_R1_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
618 # --read2_indicator '_R2_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
619 # --leading_text '' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
620 # --trailing_text ''
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
621
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
622 multiple_join_paired_ends.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
623 --input_dir 'test-data/multiple_join_paired_ends/with_barcode/' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
624 --output_dir 'test-data/multiple_join_paired_ends/output_with_barcode' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
625 --read1_indicator 'forward_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
626 --read2_indicator 'reverse_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
627 --match_barcodes \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
628 --barcode_indicator 'barcode_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
629 --leading_text '' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
630 --trailing_text ''
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
631
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
632 # multiple_split_libraries_fastq
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
633 multiple_split_libraries_fastq.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
634 --input_dir 'test-data/multiple_split_libraries_fastq/input' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
635 --output_dir 'multiple_split_libraries_fastq' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
636 --demultiplexing_method 'mapping_barcode_files' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
637 --read_indicator 'reads_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
638 --barcode_indicator 'barcodes_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
639 --mapping_indicator 'mapping_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
640 --mapping_extensions 'txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
641 --leading_text '' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
642 --trailing_text '' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
643 --sampleid_indicator '.'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
644
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
645 multiple_split_libraries_fastq.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
646 --input_dir 'test-data/multiple_split_libraries_fastq/input' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
647 --output_dir 'multiple_split_libraries_fastq_with_parameter_file' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
648 --demultiplexing_method 'mapping_barcode_files' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
649 --parameter_fp 'test-data/multiple_split_libraries_fastq/qiime_parameters.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
650 --read_indicator 'reads_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
651 --barcode_indicator 'barcodes_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
652 --mapping_indicator 'mapping_' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
653 --mapping_extensions 'txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
654 --leading_text '' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
655 --trailing_text '' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
656 --sampleid_indicator '.'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
657
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
658 # pick_closed_reference_otus
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
659 pick_closed_reference_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
660 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
661 --output_dir 'pick_closed_reference_otus' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
662 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
663 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
664 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
665 -i 'pick_closed_reference_otus/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
666 -o 'test-data/pick_closed_reference_otus/basic_otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
667 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
668
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
669 pick_closed_reference_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
670 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
671 --output_dir 'pick_closed_reference_otus_sortmerna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
672 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
673 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
674 --parameter_fp 'test-data/pick_closed_reference_otus/sortmerna_params.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
675 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
676 -i 'pick_closed_reference_otus_sortmerna/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
677 -o 'test-data/pick_closed_reference_otus/sortmerna_otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
678 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
679
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
680 pick_closed_reference_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
681 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
682 --output_dir 'pick_closed_reference_otus_assign_taxonomy' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
683 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
684 --assign_taxonomy
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
685 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
686 -i 'pick_closed_reference_otus_assign_taxonomy/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
687 -o 'test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
688 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
689
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
690 pick_closed_reference_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
691 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
692 --output_dir 'pick_closed_reference_otus_suppress_taxonomy_assignment' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
693 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
694 --suppress_taxonomy_assignment
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
695 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
696 -i 'pick_closed_reference_otus_suppress_taxonomy_assignment/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
697 -o 'test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
698 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
699
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
700 # pick_open_reference_otus
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
701 pick_open_reference_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
702 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
703 -o pick_open_reference_otus_1 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
704 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
705 --otu_picking_method 'uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
706 --new_ref_set_id 'New' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
707 --parallel \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
708 --percent_subsample '0.001' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
709 --prefilter_percent_id '0.0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
710 --minimum_failure_threshold '100000' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
711 --min_otu_size '2'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
712 cp pick_open_reference_otus_1/final_otu_map.txt 'test-data/pick_open_reference_otus/1_final_otu_map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
713 cp pick_open_reference_otus_1/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/1_final_otu_map_mc.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
714 cp pick_open_reference_otus_1/rep_set.tre 'test-data/pick_open_reference_otus/1_rep_set_tree.tre'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
715 rm -rf pick_open_reference_otus_1
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
716
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
717 pick_open_reference_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
718 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
719 -o pick_open_reference_otus_2 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
720 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
721 --otu_picking_method 'uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
722 --new_ref_set_id 'New' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
723 --parallel \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
724 --percent_subsample '0.001' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
725 --prefilter_percent_id '0.0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
726 --minimum_failure_threshold '100000' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
727 --min_otu_size '3' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
728 --suppress_taxonomy_assignment \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
729 --suppress_align_and_tree
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
730 cp pick_open_reference_otus_2/final_otu_map.txt 'test-data/pick_open_reference_otus/2_final_otu_map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
731 cp pick_open_reference_otus_2/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/2_final_otu_map_mc.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
732 rm -rf pick_open_reference_otus_2
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
733
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
734 pick_open_reference_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
735 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
736 -o pick_open_reference_otus_3 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
737 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
738 --otu_picking_method 'uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
739 --new_ref_set_id 'New' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
740 --parallel \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
741 --percent_subsample '0.001' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
742 --prefilter_percent_id '0.0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
743 --minimum_failure_threshold '100000' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
744 --min_otu_size '10' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
745 --suppress_taxonomy_assignment
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
746 cp pick_open_reference_otus_3/final_otu_map.txt 'test-data/pick_open_reference_otus/3_final_otu_map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
747 cp pick_open_reference_otus_3/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/3_final_otu_map_mc.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
748 cp pick_open_reference_otus_3/rep_set.tre 'test-data/pick_open_reference_otus/3_rep_set_tree.tre'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
749 rm -rf pick_open_reference_otus_3
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
750
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
751 # pick_otus
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
752 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
753 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
754 -o 'pick_otus_uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
755 --otu_picking_method 'uclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
756 --similarity "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
757 --denovo_otu_id_prefix "denovo" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
758 --max_accepts "1" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
759 --max_rejects "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
760 --stepwords "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
761 --word_length "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
762 --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
763
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
764 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
765 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
766 -o 'pick_otus_sortmerna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
767 --otu_picking_method "sortmerna" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
768 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
769 --sortmerna_e_value "1" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
770 --sortmerna_coverage "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
771 --sortmerna_tabular \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
772 --sortmerna_best_N_alignments "1" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
773 --sortmerna_max_pos "10000" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
774 --similarity "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
775 --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
776
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
777 #pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
778 # -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
779 # -o 'pick_otus_mothur' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
780 # --otu_picking_method "mothur" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
781 # --clustering_algorithm "furthest" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
782 # --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
783
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
784 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
785 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
786 -o 'pick_otus_trie' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
787 --otu_picking_method "trie" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
788 --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
789
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
790 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
791 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
792 -o 'pick_otus_uclust_ref' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
793 --otu_picking_method "uclust_ref" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
794 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
795 --similarity "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
796 --max_accepts "1" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
797 --max_rejects "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
798 --stepwords "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
799 --word_length "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
800 --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
801
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
802 #pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
803 # -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
804 # -o 'pick_otus_blast' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
805 # --otu_picking_method "blast" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
806 # --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
807 # --similarity "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
808 # --max_e_value_blast "1e-10" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
809 # --min_aligned_percent "0.5" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
810 # --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
811
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
812 # pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
813 # -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
814 # -o 'pick_otus_sumaclust' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
815 # --otu_picking_method "sumaclust" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
816 # --similarity "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
817 # --sumaclust_l \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
818 # --denovo_otu_id_prefix "denovo" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
819 # --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
820
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
821 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
822 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
823 -o 'pick_otus_swarm' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
824 --otu_picking_method "swarm" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
825 --denovo_otu_id_prefix "denovo" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
826 --swarm_resolution "1" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
827 --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
828
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
829 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
830 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
831 -o 'pick_otus_prefix_suffix' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
832 --otu_picking_method "prefix_suffix" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
833 --prefix_length "50" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
834 --suffix_length "50" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
835 --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
836
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
837 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
838 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
839 -o 'pick_otus_cdhit' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
840 --otu_picking_method "cdhit" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
841 --similarity "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
842 --non_chimeras_retention "union"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
843
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
844 pick_otus.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
845 -i 'test-data/pick_otus/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
846 -o 'pick_otus_uclust_intersection' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
847 --otu_picking_method "uclust" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
848 --similarity "0.97" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
849 --denovo_otu_id_prefix "denovo" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
850 --max_accepts "1" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
851 --max_rejects "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
852 --stepwords "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
853 --word_length "8" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
854 --non_chimeras_retention "intersection"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
855
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
856 # pick_rep_set
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
857 pick_rep_set.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
858 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
859 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
860 --rep_set_picking_method 'first' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
861 --sort_by 'otu' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
862 --result_fp 'test-data/pick_rep_set/first_otu_fasta.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
863 --log_fp 'test-data/pick_rep_set/first_otu_fasta.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
864
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
865 pick_rep_set.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
866 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
867 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
868 --reference_seqs_fp 'test-data/pick_rep_set/refseqs.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
869 --rep_set_picking_method 'first' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
870 --sort_by 'otu' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
871 --result_fp 'test-data/pick_rep_set/first_otu_fasta_ref.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
872 --log_fp 'test-data/pick_rep_set/first_otu_fasta_ref.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
873
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
874 pick_rep_set.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
875 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
876 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
877 --rep_set_picking_method 'longest' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
878 --sort_by 'otu' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
879 --result_fp 'test-data/pick_rep_set/longest_otu_fasta.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
880 --log_fp 'test-data/pick_rep_set/longest_otu_fasta.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
881
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
882 pick_rep_set.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
883 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
884 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
885 --rep_set_picking_method 'most_abundant' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
886 --sort_by 'otu' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
887 --result_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
888 --log_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
889
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
890 pick_rep_set.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
891 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
892 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
893 --rep_set_picking_method 'random' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
894 --sort_by 'otu' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
895 --result_fp 'test-data/pick_rep_set/random_otu_fasta.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
896 --log_fp 'test-data/pick_rep_set/random_otu_fasta.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
897
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
898 pick_rep_set.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
899 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
900 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
901 --rep_set_picking_method 'first' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
902 --sort_by 'seq_id' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
903 --result_fp 'test-data/pick_rep_set/first_seq_id_fasta.fasta' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
904 --log_fp 'test-data/pick_rep_set/first_seq_id_fasta.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
905
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
906 # plot_taxa_summary
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
907 plot_taxa_summary.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
908 --counts_fname 'test-data/plot_taxa_summary/phylum.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
909 --dir_path 'test-data/plot_taxa_summary/phylum' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
910 --labels 'phylum' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
911 --num_categories '20' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
912 --background_color 'white' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
913 --dpi '80' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
914 --x_width '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
915 --y_height '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
916 --bar_width '0.75' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
917 --type_of_file 'png' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
918 --chart_type 'area,bar,pie' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
919 --resize_nth_label '0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
920 --label_type 'categorical'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
921
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
922 plot_taxa_summary.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
923 --counts_fname 'test-data/plot_taxa_summary/phylum.txt,test-data/plot_taxa_summary/class.txt,test-data/plot_taxa_summary/genus.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
924 --dir_path 'test-data/plot_taxa_summary/phylum_class_genus' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
925 --labels 'Phylum,Class,Genus' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
926 --num_categories '20' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
927 --background_color 'white' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
928 --dpi '80' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
929 --x_width '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
930 --y_height '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
931 --bar_width '0.75' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
932 --type_of_file 'png' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
933 --chart_type 'area,bar,pie' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
934 --resize_nth_label '0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
935 --label_type 'categorical'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
936
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
937 plot_taxa_summary.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
938 --counts_fname 'test-data/plot_taxa_summary/class.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
939 --dir_path 'test-data/plot_taxa_summary/class' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
940 --labels 'Class' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
941 --num_categories '10' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
942 --background_color 'white' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
943 --dpi '80' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
944 --x_width '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
945 --y_height '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
946 --bar_width '0.75' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
947 --chart_type 'pie' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
948 --type_of_file 'svg' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
949 --include_html_legend \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
950 --resize_nth_label '0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
951 --label_type 'categorical'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
952
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
953 plot_taxa_summary.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
954 --counts_fname 'test-data/plot_taxa_summary/class.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
955 --dir_path 'test-data/plot_taxa_summary/class_colorby' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
956 --labels 'Class' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
957 --num_categories '20' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
958 --colorby 'PC.636,PC.635' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
959 --background_color 'white' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
960 --dpi '80' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
961 --x_width '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
962 --y_height '12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
963 --bar_width '0.75' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
964 --type_of_file 'pdf' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
965 --chart_type 'area,bar,pie' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
966 --resize_nth_label '0' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
967 --label_type 'categorical'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
968
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
969 # split_libraries
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
970 split_libraries.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
971 --map 'test-data/split_libraries/mapping_file.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
972 -o split_libraries \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
973 --fasta 'test-data/split_libraries/reads_1.fna,test-data/split_libraries/reads_2.fna' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
974 --qual 'test-data/split_libraries/reads_1.qual,test-data/split_libraries/reads_2.qual' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
975 --min_qual_score 25 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
976 --qual_score_window 0 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
977 --record_qual_scores \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
978 --min_seq_length 200 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
979 --max_seq_length 1000 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
980 --max_ambig 6 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
981 --max_homopolymer 6 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
982 --max_primer_mismatch 0 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
983 --barcode_type 'golay_12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
984 --max_barcode_errors 1.5 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
985 --start_numbering_at 1
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
986 cp split_libraries/seqs.fna 'test-data/split_libraries/seqs.fna'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
987 cp split_libraries/split_library_log.txt 'test-data/split_libraries/split_library_log'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
988 cp split_libraries/histograms.txt 'test-data/split_libraries/histograms.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
989 cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
990 rm -rf split_libraries
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
991
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
992 # split_libraries_fastq
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
993 split_libraries_fastq.py \
5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
994 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
995 -o split_libraries_1 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
996 --mapping_fps 'test-data/split_libraries_fastq/map.txt' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
997 --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
998 --max_bad_run_length 3 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
999 --min_per_read_length_fraction 0.75 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1000 --sequence_max_n 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1001 --start_seq_id 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1002 --rev_comp_mapping_barcodes \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1003 --phred_quality_threshold 19 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1004 --barcode_type 'golay_12' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1005 --max_barcode_errors 1.5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1006 rm -rf split_libraries_1
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1007
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1008 split_libraries_fastq.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1009 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1010 -o split_libraries_2 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1011 --mapping_fps 'test-data/split_libraries_fastq/map.txt' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1012 --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \
0
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1013 --store_qual_scores \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1014 --store_demultiplexed_fastq \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1015 --max_bad_run_length 3 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1016 --min_per_read_length_fraction 0.75 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1017 --sequence_max_n 0 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1018 --start_seq_id 0 \
5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1019 --rev_comp_mapping_barcodes \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1020 --phred_quality_threshold 19 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1021 --barcode_type 'golay_12' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1022 --max_barcode_errors 1.5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1023 rm -rf split_libraries_2
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1024
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1025 split_libraries_fastq.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1026 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1027 -o split_libraries_3 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1028 --mapping_fps 'test-data/split_libraries_fastq/map.txt,test-data/split_libraries_fastq/map.txt' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1029 --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz,test-data/split_libraries_fastq/lane2_barcode.fastq.gz' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1030 --max_bad_run_length 3 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1031 --min_per_read_length_fraction 0.75 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1032 --sequence_max_n 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1033 --start_seq_id 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1034 --rev_comp_mapping_barcodes \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1035 --phred_quality_threshold 19 \
0
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1036 --barcode_type 'golay_12' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1037 --max_barcode_errors 1.5
5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1038 rm -rf split_libraries_3
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1039
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1040 split_libraries_fastq.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1041 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1042 -o split_libraries_4 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1043 --sample_ids 'my.sample.1' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1044 --max_bad_run_length 3 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1045 --min_per_read_length_fraction 0.75 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1046 --sequence_max_n 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1047 --start_seq_id 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1048 --rev_comp_mapping_barcodes \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1049 --phred_quality_threshold 19 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1050 --barcode_type 'not-barcoded' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1051 --max_barcode_errors 1.5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1052 rm -rf split_libraries_4
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1053
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1054 split_libraries_fastq.py \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1055 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1056 -o split_libraries_5 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1057 --sample_ids 'my.sample.1,my.sample.2' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1058 --max_bad_run_length 3 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1059 --min_per_read_length_fraction 0.75 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1060 --sequence_max_n 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1061 --start_seq_id 0 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1062 --rev_comp_mapping_barcodes \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1063 --phred_quality_threshold 19 \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1064 --barcode_type 'not-barcoded' \
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1065 --max_barcode_errors 1.5
98614f0549e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents: 3
diff changeset
1066 rm -rf split_libraries_5
0
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1067
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1068 # summarize_taxa
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1069 cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1070 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1071
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1072 summarize_taxa.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1073 -i 'test-data/summarize_taxa/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1074 -o summarize_taxa_1 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1075 -L '2,3,4,5,6' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1076 -m 'test-data/summarize_taxa/map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1077 --md_identifier "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1078 --delimiter ";"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1079 cp summarize_taxa_1/*_L2.txt "test-data/summarize_taxa/1_L2.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1080 cp summarize_taxa_1/*_L3.txt "test-data/summarize_taxa/1_L3.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1081 cp summarize_taxa_1/*_L4.txt "test-data/summarize_taxa/1_L4.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1082 cp summarize_taxa_1/*_L5.txt "test-data/summarize_taxa/1_L5.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1083 cp summarize_taxa_1/*_L6.txt "test-data/summarize_taxa/1_L6.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1084 rm -rf summarize_taxa_1
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1085
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1086 summarize_taxa.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1087 -i 'test-data/summarize_taxa/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1088 -o summarize_taxa_2 \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1089 -L '3,6' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1090 --md_identifier "taxonomy" \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1091 --delimiter ";"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1092 cp summarize_taxa_2/*_L3.txt "test-data/summarize_taxa/2_L3.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1093 cp summarize_taxa_2/*_L6.txt "test-data/summarize_taxa/2_L6.txt"
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1094 rm -rf summarize_taxa_2
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1095
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1096 # summarize_taxa_through_plots
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1097 summarize_taxa_through_plots.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1098 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1099 --output_dir summarize_taxa_through_plots_mapping \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1100 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1101 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1102 -i 'summarize_taxa_through_plots_mapping/otu_table_L2.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1103 -o 'summarize_taxa_through_plots_mapping/otu_table_L2_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1104 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1105 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1106 -i 'summarize_taxa_through_plots_mapping/otu_table_L3.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1107 -o 'summarize_taxa_through_plots_mapping/otu_table_L3_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1108 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1109 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1110 -i 'summarize_taxa_through_plots_mapping/otu_table_L4.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1111 -o 'summarize_taxa_through_plots_mapping/otu_table_L4_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1112 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1113 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1114 -i 'summarize_taxa_through_plots_mapping/otu_table_L5.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1115 -o 'summarize_taxa_through_plots_mapping/otu_table_L5_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1116 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1117 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1118 -i 'summarize_taxa_through_plots_mapping/otu_table_L6.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1119 -o 'summarize_taxa_through_plots_mapping/otu_table_L6_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1120 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1121 cp summarize_taxa_through_plots_mapping/*.txt test-data/summarize_taxa_through_plots/mapping/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1122 cp summarize_taxa_through_plots_mapping/*_json.biom test-data/summarize_taxa_through_plots/mapping/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1123 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping/area_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1124 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping/bar_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1125
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1126 summarize_taxa_through_plots.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1127 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1128 --output_dir summarize_taxa_through_plots_mapping_categories \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1129 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1130 --mapping_category 'Treatment'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1131 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1132 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1133 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1134 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1135 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1136 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1137 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1138 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1139 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1140 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1141 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1142 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1143 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1144 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1145 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1146 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1147 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1148 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1149 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1150 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1151 cp summarize_taxa_through_plots_mapping_categories/*.txt test-data/summarize_taxa_through_plots/mapping_categories/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1152 cp summarize_taxa_through_plots_mapping_categories/*_json.biom test-data/summarize_taxa_through_plots/mapping_categories/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1153 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1154 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1155
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1156 summarize_taxa_through_plots.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1157 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1158 --output_dir summarize_taxa_through_plots_mapping_sort \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1159 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1160 --sort
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1161 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1162 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1163 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1164 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1165 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1166 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1167 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1168 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1169 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1170 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1171 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1172 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1173 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1174 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1175 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1176 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1177 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1178 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1179 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1180 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1181 cp summarize_taxa_through_plots_mapping_sort/*.txt test-data/summarize_taxa_through_plots/mapping_sort/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1182 cp summarize_taxa_through_plots_mapping_sort/*_json.biom test-data/summarize_taxa_through_plots/mapping_sort/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1183 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1184 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1185
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1186 summarize_taxa_through_plots.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1187 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1188 --output_dir summarize_taxa_through_plots_without_mapping
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1189 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1190 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L2.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1191 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L2_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1192 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1193 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1194 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L3.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1195 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L3_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1196 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1197 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1198 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L4.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1199 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L4_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1200 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1201 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1202 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L5.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1203 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L5_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1204 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1205 biom convert \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1206 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L6.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1207 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L6_json.biom' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1208 --to-json
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1209 cp summarize_taxa_through_plots_without_mapping/*.txt test-data/summarize_taxa_through_plots/without_mapping/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1210 cp summarize_taxa_through_plots_without_mapping/*_json.biom test-data/summarize_taxa_through_plots/without_mapping/
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1211 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/area_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1212 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1213
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1214 # upgma_cluster
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1215 upgma_cluster.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1216 --input_path 'test-data/upgma_cluster/' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1217 --output_path 'test-data/upgma_cluster/'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1218
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1219 # validate_mapping_file
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1220 validate_mapping_file.py \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1221 -m 'test-data/validate_mapping_file/map.tsv' \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1222 -o validate_mapping_file_output \
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1223 -c '_'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1224 cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1225 cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1226 cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt'
56adf8db7ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1227 rm -rf validate_mapping_file_output