Mercurial > repos > iuc > qiime_jackknifed_beta_diversity
annotate generate_test_data.sh @ 3:b63216cf3245 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
author | iuc |
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date | Thu, 22 Jun 2017 06:58:50 -0400 |
parents | f9df45b8425a |
children | 205f4c9739c0 |
rev | line source |
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0
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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1 #!/usr/bin/env bash |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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2 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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3 # Data are from test data in https://github.com/biocore/qiime |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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4 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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5 # align_seqs |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
6 align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
7 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
8 -o 'align_seqs_pynast_uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
9 --alignment_method 'pynast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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10 --pairwise_alignment_method 'uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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11 --template_fp 'test-data/align_seqs/core_set_aligned.fasta.imputed' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
12 --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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13 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
14 align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
15 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
16 -o 'align_seqs_pynast_muscle' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
17 --alignment_method 'pynast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
18 --pairwise_alignment_method 'muscle' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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19 --min_length '50' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
20 --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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21 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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22 align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
23 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
24 -o 'align_seqs_pynast_pair_hmm' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
25 --alignment_method 'pynast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
26 --pairwise_alignment_method 'pair_hmm' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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27 --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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28 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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29 #align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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30 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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31 # -o 'align_seqs_pynast_clustal' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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32 # --alignment_method 'pynast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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33 # --pairwise_alignment_method 'clustal' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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34 # --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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35 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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36 align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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37 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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38 -o 'align_seqs_pynast_blast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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39 --alignment_method 'pynast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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40 --pairwise_alignment_method 'blast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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41 --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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42 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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43 align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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44 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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45 -o 'align_seqs_pynast_mafft' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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46 --alignment_method 'pynast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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47 --pairwise_alignment_method 'mafft' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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48 --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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49 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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50 #align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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51 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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52 # -o 'align_seqs_infernal' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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53 # --alignment_method 'infernal' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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54 # --template_fp 'test-data/align_seqs/seed.16s.reference_model.sto' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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55 # --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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56 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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57 #align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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58 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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59 # -o 'align_seqs_clustalw' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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60 # --alignment_method 'clustalw' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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61 # --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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62 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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63 align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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64 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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65 -o 'align_seqs_muscle' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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66 --alignment_method 'muscle' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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67 --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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68 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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69 align_seqs.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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70 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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71 -o 'align_seqs_mafft' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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72 --alignment_method 'mafft' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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73 --min_percent_id '0.75' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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74 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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75 #alpha_rarefaction |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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76 alpha_rarefaction.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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77 --otu_table_fp "test-data/alpha_rarefaction/otu_table.biom" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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78 --mapping_fp "test-data/alpha_rarefaction/mapping_file.txt" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
79 -o alpha_rarefaction \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
80 --num_steps '2' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
81 --tree_fp "test-data/alpha_rarefaction/rep_set.tre" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
82 --min_rare_depth '10' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
83 --max_rare_depth '50' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
84 --retain_intermediate_files |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
85 rm -rf alpha_rarefaction |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
86 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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|
87 # assign_taxonomy |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
88 assign_taxonomy.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
89 --input_fasta_fp 'test-data/assign_taxonomy/uclust_input_seqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
90 --assignment_method 'uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
91 --min_consensus_fraction '0.51' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
92 --similarity '0.9' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
93 --uclust_max_accepts '3' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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94 -o assign_taxonomy_uclust |
3
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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|
95 ls assign_taxonomy_uclust |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
changeset
|
96 md5sum 'assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt' |
0
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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97 rm -rf assign_taxonomy_uclust |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
|
98 |
3
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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99 assign_taxonomy.py \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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|
100 --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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0
diff
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101 --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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102 --assignment_method 'mothur' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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103 --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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104 --confidence '0.5' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
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diff
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105 -o assign_taxonomy_mothur |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
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diff
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106 ls assign_taxonomy_mothur |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
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diff
changeset
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107 md5sum 'assign_taxonomy_mothur/mothur_repr_set_seqs_tax_assignments.txt' |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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108 rm -rf assign_taxonomy_mothur |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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109 |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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0
diff
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110 assign_taxonomy.py \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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0
diff
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111 --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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0
diff
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112 --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
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diff
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113 --assignment_method 'mothur' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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diff
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114 --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
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diff
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115 --blast_e_value '0.001' \ |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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diff
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116 -o assign_taxonomy_blast |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
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diff
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117 ls assign_taxonomy_blast |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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|
118 md5sum 'assign_taxonomy_blast/mothur_repr_set_seqs_tax_assignments.txt' |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
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diff
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119 rm -rf assign_taxonomy_blast |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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|
120 |
0
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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121 #assign_taxonomy.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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|
122 # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
123 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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124 # --assignment_method 'rdp' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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|
125 # --confidence '3' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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126 # -o assign_taxonomy_rdp |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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|
127 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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128 #assign_taxonomy.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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129 # --input_fasta_fp 'test-data/assign_taxonomy/rtax_ref_seq_set.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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130 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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131 # --assignment_method 'rtax' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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132 # --read_1_seqs_fp 'test-data/assign_taxonomy/read_1.seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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133 # --read_2_seqs_fp 'test-data/assign_taxonomy/read_2.seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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134 # --single_ok \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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135 # --no_single_ok_generic \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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136 # --read_id_regex "\S+\s+(\S+)" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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137 # --amplicon_id_regex "(\S+)\s+(\S+?)\/" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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138 # --header_id_regex "\S+\s+(\S+?)\/" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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139 # -o assign_taxonomy_rtax |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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140 #ls assign_taxonomy_rtax |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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141 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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142 assign_taxonomy.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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143 --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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144 --assignment_method 'sortmerna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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145 --min_consensus_fraction "0.51" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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146 --similarity "0.9" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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147 --sortmerna_e_value "1.0" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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148 --sortmerna_coverage "0.9" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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149 --sortmerna_best_N_alignments "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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150 -o assign_taxonomy_sortmerna |
3
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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|
151 ls assign_taxonomy_sortmerna |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
0
diff
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152 md5sum 'assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt' |
b63216cf3245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
iuc
parents:
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153 md5sum 'assign_taxonomy_sortmerna/sortmerna_map.blast' |
0
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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154 rm -rf assign_taxonomy_sortmerna |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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155 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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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' \ |
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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 |
f9df45b8425a
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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 \ |
f9df45b8425a
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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' \ |
f9df45b8425a
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170 --tree_path 'test-data/beta_diversity/rep_set.tre' |
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171 md5 'beta_diversity_2/canberra_otu_table.txt' |
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172 md5 'beta_diversity_2/pearson_otu_table.txt' |
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173 rm -rf beta_diversity_2 |
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174 |
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175 #beta_diversity_through_plots |
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176 beta_diversity_through_plots.py \ |
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177 --otu_table_fp 'test-data/beta_diversity_through_plots/otu_table.biom' \ |
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178 --mapping_fp 'test-data/beta_diversity_through_plots/map.txt' \ |
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179 --output_dir beta_diversity_through_plots \ |
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180 --tree_fp 'test-data/beta_diversity_through_plots/rep_set.tre' \ |
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181 --parallel |
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182 cp beta_diversity_through_plots/unweighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/' |
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183 cp beta_diversity_through_plots/unweighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/' |
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184 cp beta_diversity_through_plots/weighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/' |
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185 cp beta_diversity_through_plots/weighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/' |
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186 rm -rf beta_diversity_through_plots |
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187 |
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188 # compare_categories |
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189 compare_categories.py \ |
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190 --method 'adonis' \ |
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191 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \ |
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192 --mapping_file 'test-data/compare_categories/map.txt' \ |
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193 --categories 'Treatment' \ |
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194 -o compare_categories_1 \ |
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195 --num_permutations '999' |
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196 cp compare_categories_1/adonis_results.txt "test-data/compare_categories/adonis_results.txt" |
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197 rm -rf compare_categories_1 |
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198 |
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199 compare_categories.py \ |
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200 --method 'dbrda' \ |
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201 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \ |
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202 --mapping_file 'test-data/compare_categories/map.txt' \ |
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203 --categories 'Treatment' \ |
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204 -o compare_categories_2 \ |
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205 --num_permutations '99' |
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206 cp compare_categories_2/* "test-data/compare_categories/" |
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207 rm -rf compare_categories_2 |
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208 |
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209 # core_diversity_analyses |
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210 core_diversity_analyses.py \ |
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211 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \ |
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212 -o core_diversity_analyses_1 \ |
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213 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \ |
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214 --sampling_depth 22 \ |
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215 --tree_fp 'test-data/core_diversity_analyses/rep_set.tre' |
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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' |
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217 rm -rf core_diversity_analyses_1 |
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218 |
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219 core_diversity_analyses.py \ |
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220 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \ |
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221 -o core_diversity_analyses_2 \ |
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222 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \ |
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223 --sampling_depth 22 \ |
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224 --nonphylogenetic_diversity \ |
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225 --suppress_taxa_summary \ |
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226 --suppress_beta_diversity \ |
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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 |
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231 # filter_alignment |
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232 filter_alignment.py \ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
233 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
234 -o 'filter_alignment_default' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
235 --allowed_gap_frac '0.999999' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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236 --threshold '3.0' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
237 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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238 filter_alignment.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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239 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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240 -o 'filter_alignment_without_mask_filter_and_outliers' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
241 --suppress_lane_mask_filter \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
242 --allowed_gap_frac '0.999999' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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243 --remove_outliers \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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244 --threshold '3.0' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
245 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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246 filter_alignment.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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247 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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248 -o 'filter_alignment_entropy' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
249 --allowed_gap_frac '0.999999' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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250 --threshold '3.0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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251 --entropy_threshold '0.1' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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252 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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253 # filter_fasta |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
254 filter_fasta.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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255 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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256 --output_fasta_fp 'filter_fasta_otu_map.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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257 --otu_map 'test-data/filter_fasta/otu_map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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258 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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259 filter_fasta.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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260 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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261 --output_fasta_fp 'filter_fasta_otu_map_negate.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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262 --otu_map 'test-data/filter_fasta/otu_map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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263 --negate |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
264 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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265 filter_fasta.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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266 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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267 --output_fasta_fp 'filter_fasta_seq_id.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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268 --seq_id_fp 'test-data/filter_fasta/seqs_to_keep.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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269 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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270 filter_fasta.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
271 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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272 --output_fasta_fp 'filter_fasta_otu_table.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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273 --biom_fp 'test-data/filter_fasta/otu_table.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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|
274 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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275 filter_fasta.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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276 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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277 --output_fasta_fp 'filter_fasta_subject_fasta.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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278 --subject_fasta_fp 'test-data/filter_fasta/sl_inseqs.fasta' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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|
279 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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280 filter_fasta.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
281 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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282 --output_fasta_fp 'filter_fasta_seq_id_prefix.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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283 --seq_id_prefix 'S5' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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|
284 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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285 filter_fasta.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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286 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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287 --output_fasta_fp 'filter_fasta_sample_id.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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288 --sample_id_fp 'test-data/filter_fasta/map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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|
289 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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290 # filter_otus_from_otu_table |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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291 filter_otus_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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292 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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293 --min_count '2' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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294 --max_count '1000' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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295 --min_samples '5' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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296 --max_samples '350' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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297 --output_fp 'test-data/filter_otus_from_otu_table/filtered_otu_table.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
|
298 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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299 filter_otus_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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300 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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301 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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302 --output_fp 'test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
|
303 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
304 filter_otus_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
305 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
|
306 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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307 --negate_ids_to_exclude \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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308 --output_fp 'test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
|
309 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
310 # filter_samples_from_otu_table |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
311 filter_samples_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
312 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
313 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
314 --min_count '150' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
315 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
316 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
317 -o 'test-data/filter_samples_from_otu_table/abundance_min.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
318 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
319 rm 'test-data/filter_samples_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
320 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
321 filter_samples_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
322 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
323 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
324 --min_count '0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
325 --max_count '149' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
326 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
327 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
328 -o 'test-data/filter_samples_from_otu_table/abundance_max.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
329 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
330 rm 'test-data/filter_samples_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
331 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
332 filter_samples_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
333 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
334 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
335 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
336 --output_mapping_fp 'test-data/filter_samples_from_otu_table/metadata_positive.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
337 -s 'Treatment:Control' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
338 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
339 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
340 -o 'test-data/filter_samples_from_otu_table/metadata_positive.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
341 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
342 rm 'test-data/filter_samples_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
343 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
344 filter_samples_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
345 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
346 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
347 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
348 -s 'Treatment:*,!Control' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
349 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
350 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
351 -o 'test-data/filter_samples_from_otu_table/metadata_negative.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
352 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
353 rm 'test-data/filter_samples_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
354 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
355 filter_samples_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
356 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
357 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
358 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
359 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
360 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
361 -o 'test-data/filter_samples_from_otu_table/id_positive.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
362 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
363 rm 'test-data/filter_samples_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
364 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
365 filter_samples_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
366 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
367 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
368 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
369 --negate_sample_id_fp |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
370 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
371 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
372 -o 'test-data/filter_samples_from_otu_table/id_negative.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
373 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
374 rm 'test-data/filter_samples_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
375 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
376 # filter_taxa_from_otu_table |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
377 filter_taxa_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
378 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
379 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
380 --positive_taxa 'p__Bacteroidetes,p__Firmicutes' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
381 --metadata_field 'taxonomy' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
382 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
383 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
384 -o 'test-data/filter_taxa_from_otu_table/positive_taxa.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
385 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
386 rm 'test-data/filter_taxa_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
387 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
388 filter_taxa_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
389 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
390 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
391 --negative_taxa 'p__Bacteroidetes,p__Firmicutes' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
392 --metadata_field 'taxonomy' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
393 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
394 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
395 -o 'test-data/filter_taxa_from_otu_table/negative_taxa.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
396 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
397 rm 'test-data/filter_taxa_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
398 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
399 filter_taxa_from_otu_table.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
400 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
401 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
402 --positive_taxa 'p__Firmicutes' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
403 --negative_taxa 'c__Clostridia' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
404 --metadata_field 'taxonomy' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
405 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
406 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
407 -o 'test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
408 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
409 rm 'test-data/filter_taxa_from_otu_table/tmp.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
410 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
411 # jackknifed_beta_diversity |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
412 jackknifed_beta_diversity.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
413 --otu_table_fp 'test-data/jackknifed_beta_diversity/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
414 --mapping_fp 'test-data/jackknifed_beta_diversity/map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
415 -o jackknifed_beta_diversity \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
416 --seqs_per_sample '10' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
417 --tree_fp 'test-data/jackknifed_beta_diversity/rep_set.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
418 --master_tree 'consensus' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
419 --parallel |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
420 rm -rf jackknifed_beta_diversity |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
421 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
422 # make_emperor |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
423 cp 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' 'test-data/make_emperor/unweighted_unifrac_pc.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
424 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/make_emperor/map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
425 cp 'test-data/summarize_taxa/2_L3.txt' 'test-data/make_emperor/2_L3.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
426 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
427 make_emperor.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
428 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
429 -o make_emperor_1 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
430 --map_fp 'test-data/make_emperor/map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
431 --number_of_axes '10' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
432 --add_unique_columns \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
433 --number_of_segments 8 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
434 rm -rf make_emperor_1 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
435 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
436 make_emperor.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
437 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
438 -o make_emperor_2 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
439 --map_fp 'test-data/make_emperor/map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
440 --number_of_axes '10' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
441 --add_unique_columns \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
442 --number_of_segments 8 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
443 --taxa_fp 'test-data/make_emperor/2_L3.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
444 --n_taxa_to_keep 10 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
445 rm -rf make_emperor_2 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
446 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
447 # make_otu_heatmap |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
448 make_otu_heatmap.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
449 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
450 --imagetype 'pdf' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
451 --color_scheme "YlGn" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
452 --width "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
453 --height "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
454 --dpi "200" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
455 --obs_md_category "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
456 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.pdf' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
457 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
458 make_otu_heatmap.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
459 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
460 --imagetype 'png' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
461 --color_scheme "YlGn" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
462 --width "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
463 --height "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
464 --dpi "200" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
465 --obs_md_category "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
466 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.png' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
467 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
468 make_otu_heatmap.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
469 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
470 --imagetype 'svg' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
471 --color_scheme "YlGn" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
472 --width "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
473 --height "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
474 --dpi "200" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
475 --obs_md_category "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
476 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.svg' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
477 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
478 make_otu_heatmap.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
479 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
480 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
481 --imagetype 'pdf' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
482 --color_scheme "YlGn" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
483 --width "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
484 --height "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
485 --dpi "200" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
486 --obs_md_category "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
487 --output_fp 'test-data/make_otu_heatmap/sample_sorted_heatmap.pdf' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
488 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
489 make_otu_heatmap.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
490 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
491 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
492 --otu_tree 'test-data/make_otu_heatmap/rep_set.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
493 --imagetype 'pdf' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
494 --color_scheme "YlGn" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
495 --width "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
496 --height "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
497 --dpi "200" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
498 --obs_md_category "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
499 --output_fp 'test-data/make_otu_heatmap/sample_otu_sorted_heatmap.pdf' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
500 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
501 make_otu_heatmap.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
502 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
503 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
504 --category "Treatment" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
505 --imagetype 'pdf' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
506 --color_scheme "YlGn" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
507 --width "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
508 --height "5" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
509 --dpi "200" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
510 --obs_md_category "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
511 --output_fp 'test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
512 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
513 # make_phylogeny |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
514 make_phylogeny.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
515 --input_fp 'test-data/make_phylogeny/aligned.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
516 --result_fp 'test-data/make_phylogeny/fasttree_tree_method_default.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
517 --tree_method 'fasttree' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
518 --log_fp 'fasttree_tree_method_default.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
519 --root_method 'tree_method_default' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
520 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
521 make_phylogeny.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
522 --input_fp 'test-data/make_phylogeny/aligned.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
523 --result_fp 'raxml_v730.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
524 --tree_method 'raxml_v730' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
525 --log_fp 'raxml_v730.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
526 --root_method 'tree_method_default' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
527 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
528 make_phylogeny.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
529 --input_fp 'test-data/make_phylogeny/aligned.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
530 --result_fp 'test-data/make_phylogeny/muscle.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
531 --tree_method 'muscle' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
532 --log_fp 'muscle.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
533 --root_method 'tree_method_default' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
534 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
535 make_phylogeny.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
536 --input_fp 'test-data/make_phylogeny/aligned.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
537 --result_fp 'test-data/make_phylogeny/clustalw.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
538 --tree_method 'clustalw' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
539 --log_fp 'clustalw.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
540 --root_method 'tree_method_default' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
541 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
542 make_phylogeny.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
543 --input_fp 'test-data/make_phylogeny/aligned.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
544 --result_fp 'clearcut.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
545 --tree_method 'clearcut' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
546 --log_fp 'clearcut.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
547 --root_method 'tree_method_default' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
548 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
549 make_phylogeny.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
550 --input_fp 'test-data/make_phylogeny/aligned.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
551 --result_fp 'test-data/make_phylogeny/fasttree_midpoint.tre' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
552 --tree_method 'fasttree' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
553 --log_fp 'fasttree_midpoint.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
554 --root_method 'midpoint' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
555 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
556 # multiple_join_paired_ends |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
557 multiple_join_paired_ends.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
558 --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
559 --output_dir 'test-data/multiple_join_paired_ends/output_without_barcode' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
560 --read1_indicator 'forward_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
561 --read2_indicator 'reverse_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
562 --leading_text '' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
563 --trailing_text '' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
564 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
565 #multiple_join_paired_ends.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
566 # --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
567 # --output_dir 'multiple_join_paired_ends_without_barcode_parameter_files' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
568 # --parameter_fp 'test-data/multiple_join_paired_ends/qiime_parameters.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
569 # --read1_indicator '_R1_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
570 # --read2_indicator '_R2_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
571 # --leading_text '' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
572 # --trailing_text '' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
573 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
574 multiple_join_paired_ends.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
575 --input_dir 'test-data/multiple_join_paired_ends/with_barcode/' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
576 --output_dir 'test-data/multiple_join_paired_ends/output_with_barcode' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
577 --read1_indicator 'forward_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
578 --read2_indicator 'reverse_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
579 --match_barcodes \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
580 --barcode_indicator 'barcode_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
581 --leading_text '' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
582 --trailing_text '' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
583 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
584 # multiple_split_libraries_fastq |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
585 multiple_split_libraries_fastq.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
586 --input_dir 'test-data/multiple_split_libraries_fastq/input' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
587 --output_dir 'multiple_split_libraries_fastq' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
588 --demultiplexing_method 'mapping_barcode_files' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
589 --read_indicator 'reads_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
590 --barcode_indicator 'barcodes_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
591 --mapping_indicator 'mapping_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
592 --mapping_extensions 'txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
593 --leading_text '' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
594 --trailing_text '' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
595 --sampleid_indicator '.' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
596 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
597 multiple_split_libraries_fastq.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
598 --input_dir 'test-data/multiple_split_libraries_fastq/input' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
599 --output_dir 'multiple_split_libraries_fastq_with_parameter_file' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
600 --demultiplexing_method 'mapping_barcode_files' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
601 --parameter_fp 'test-data/multiple_split_libraries_fastq/qiime_parameters.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
602 --read_indicator 'reads_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
603 --barcode_indicator 'barcodes_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
604 --mapping_indicator 'mapping_' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
605 --mapping_extensions 'txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
606 --leading_text '' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
607 --trailing_text '' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
608 --sampleid_indicator '.' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
609 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
610 # pick_closed_reference_otus |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
611 pick_closed_reference_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
612 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
613 --output_dir 'pick_closed_reference_otus' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
614 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
615 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
616 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
617 -i 'pick_closed_reference_otus/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
618 -o 'test-data/pick_closed_reference_otus/basic_otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
619 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
620 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
621 pick_closed_reference_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
622 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
623 --output_dir 'pick_closed_reference_otus_sortmerna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
624 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
625 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
626 --parameter_fp 'test-data/pick_closed_reference_otus/sortmerna_params.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
627 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
628 -i 'pick_closed_reference_otus_sortmerna/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
629 -o 'test-data/pick_closed_reference_otus/sortmerna_otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
630 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
631 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
632 pick_closed_reference_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
633 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
634 --output_dir 'pick_closed_reference_otus_assign_taxonomy' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
635 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
636 --assign_taxonomy |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
637 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
638 -i 'pick_closed_reference_otus_assign_taxonomy/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
639 -o 'test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
640 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
641 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
642 pick_closed_reference_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
643 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
644 --output_dir 'pick_closed_reference_otus_suppress_taxonomy_assignment' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
645 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
646 --suppress_taxonomy_assignment |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
647 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
648 -i 'pick_closed_reference_otus_suppress_taxonomy_assignment/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
649 -o 'test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
650 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
651 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
652 # pick_open_reference_otus |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
653 pick_open_reference_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
654 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
655 -o pick_open_reference_otus_1 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
656 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
657 --otu_picking_method 'uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
658 --new_ref_set_id 'New' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
659 --parallel \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
660 --percent_subsample '0.001' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
661 --prefilter_percent_id '0.0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
662 --minimum_failure_threshold '100000' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
663 --min_otu_size '2' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
664 cp pick_open_reference_otus_1/final_otu_map.txt 'test-data/pick_open_reference_otus/1_final_otu_map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
665 cp pick_open_reference_otus_1/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/1_final_otu_map_mc.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
666 cp pick_open_reference_otus_1/rep_set.tre 'test-data/pick_open_reference_otus/1_rep_set_tree.tre' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
667 rm -rf pick_open_reference_otus_1 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
668 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
669 pick_open_reference_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
670 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
671 -o pick_open_reference_otus_2 \ |
f9df45b8425a
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/gg_13_8_79_otus.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
673 --otu_picking_method 'uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
674 --new_ref_set_id 'New' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
675 --parallel \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
676 --percent_subsample '0.001' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
677 --prefilter_percent_id '0.0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
678 --minimum_failure_threshold '100000' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
679 --min_otu_size '3' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
680 --suppress_taxonomy_assignment \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
681 --suppress_align_and_tree |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
682 cp pick_open_reference_otus_2/final_otu_map.txt 'test-data/pick_open_reference_otus/2_final_otu_map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
683 cp pick_open_reference_otus_2/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/2_final_otu_map_mc.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
684 rm -rf pick_open_reference_otus_2 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
685 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
686 pick_open_reference_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
687 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
688 -o pick_open_reference_otus_3 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
689 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
690 --otu_picking_method 'uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
691 --new_ref_set_id 'New' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
692 --parallel \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
693 --percent_subsample '0.001' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
694 --prefilter_percent_id '0.0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
695 --minimum_failure_threshold '100000' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
696 --min_otu_size '10' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
697 --suppress_taxonomy_assignment |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
698 cp pick_open_reference_otus_3/final_otu_map.txt 'test-data/pick_open_reference_otus/3_final_otu_map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
699 cp pick_open_reference_otus_3/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/3_final_otu_map_mc.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
700 cp pick_open_reference_otus_3/rep_set.tre 'test-data/pick_open_reference_otus/3_rep_set_tree.tre' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
701 rm -rf pick_open_reference_otus_3 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
702 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
703 # pick_otus |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
704 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
705 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
706 -o 'pick_otus_uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
707 --otu_picking_method 'uclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
708 --similarity "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
709 --denovo_otu_id_prefix "denovo" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
710 --max_accepts "1" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
711 --max_rejects "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
712 --stepwords "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
713 --word_length "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
714 --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
715 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
716 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
717 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
718 -o 'pick_otus_sortmerna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
719 --otu_picking_method "sortmerna" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
720 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
721 --sortmerna_e_value "1" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
722 --sortmerna_coverage "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
723 --sortmerna_tabular \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
724 --sortmerna_best_N_alignments "1" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
725 --sortmerna_max_pos "10000" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
726 --similarity "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
727 --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
728 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
729 #pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
730 # -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
731 # -o 'pick_otus_mothur' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
732 # --otu_picking_method "mothur" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
733 # --clustering_algorithm "furthest" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
734 # --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
735 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
736 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
737 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
738 -o 'pick_otus_trie' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
739 --otu_picking_method "trie" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
740 --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
741 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
742 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
743 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
744 -o 'pick_otus_uclust_ref' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
745 --otu_picking_method "uclust_ref" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
746 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
747 --similarity "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
748 --max_accepts "1" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
749 --max_rejects "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
750 --stepwords "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
751 --word_length "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
752 --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
753 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
754 #pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
755 # -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
756 # -o 'pick_otus_blast' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
757 # --otu_picking_method "blast" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
758 # --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
759 # --similarity "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
760 # --max_e_value_blast "1e-10" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
761 # --min_aligned_percent "0.5" \ |
f9df45b8425a
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" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
763 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
764 # pick_otus.py \ |
f9df45b8425a
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' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
766 # -o 'pick_otus_sumaclust' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
767 # --otu_picking_method "sumaclust" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
768 # --similarity "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
769 # --sumaclust_l \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
770 # --denovo_otu_id_prefix "denovo" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
771 # --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
772 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
773 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
774 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
775 -o 'pick_otus_swarm' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
776 --otu_picking_method "swarm" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
777 --denovo_otu_id_prefix "denovo" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
778 --swarm_resolution "1" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
779 --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
780 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
781 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
782 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
783 -o 'pick_otus_prefix_suffix' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
784 --otu_picking_method "prefix_suffix" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
785 --prefix_length "50" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
786 --suffix_length "50" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
787 --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
788 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
789 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
790 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
791 -o 'pick_otus_cdhit' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
792 --otu_picking_method "cdhit" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
793 --similarity "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
794 --non_chimeras_retention "union" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
795 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
796 pick_otus.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
797 -i 'test-data/pick_otus/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
798 -o 'pick_otus_uclust_intersection' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
799 --otu_picking_method "uclust" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
800 --similarity "0.97" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
801 --denovo_otu_id_prefix "denovo" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
802 --max_accepts "1" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
803 --max_rejects "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
804 --stepwords "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
805 --word_length "8" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
806 --non_chimeras_retention "intersection" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
807 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
808 # pick_rep_set |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
809 pick_rep_set.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
810 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
811 --fasta_file 'test-data/pick_rep_set/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
812 --rep_set_picking_method 'first' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
813 --sort_by 'otu' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
814 --result_fp 'test-data/pick_rep_set/first_otu_fasta.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
815 --log_fp 'test-data/pick_rep_set/first_otu_fasta.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
816 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
817 pick_rep_set.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
818 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
819 --fasta_file 'test-data/pick_rep_set/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
820 --reference_seqs_fp 'test-data/pick_rep_set/refseqs.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
821 --rep_set_picking_method 'first' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
822 --sort_by 'otu' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
823 --result_fp 'test-data/pick_rep_set/first_otu_fasta_ref.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
824 --log_fp 'test-data/pick_rep_set/first_otu_fasta_ref.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
825 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
826 pick_rep_set.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
827 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
828 --fasta_file 'test-data/pick_rep_set/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
829 --rep_set_picking_method 'longest' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
830 --sort_by 'otu' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
831 --result_fp 'test-data/pick_rep_set/longest_otu_fasta.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
832 --log_fp 'test-data/pick_rep_set/longest_otu_fasta.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
833 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
834 pick_rep_set.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
835 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
836 --fasta_file 'test-data/pick_rep_set/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
837 --rep_set_picking_method 'most_abundant' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
838 --sort_by 'otu' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
839 --result_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
840 --log_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
841 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
842 pick_rep_set.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
843 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
844 --fasta_file 'test-data/pick_rep_set/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
845 --rep_set_picking_method 'random' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
846 --sort_by 'otu' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
847 --result_fp 'test-data/pick_rep_set/random_otu_fasta.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
848 --log_fp 'test-data/pick_rep_set/random_otu_fasta.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
849 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
850 pick_rep_set.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
851 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
852 --fasta_file 'test-data/pick_rep_set/seqs.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
853 --rep_set_picking_method 'first' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
854 --sort_by 'seq_id' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
855 --result_fp 'test-data/pick_rep_set/first_seq_id_fasta.fasta' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
856 --log_fp 'test-data/pick_rep_set/first_seq_id_fasta.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
857 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
858 # plot_taxa_summary |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
859 plot_taxa_summary.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
860 --counts_fname 'test-data/plot_taxa_summary/phylum.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
861 --dir_path 'test-data/plot_taxa_summary/phylum' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
862 --labels 'phylum' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
863 --num_categories '20' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
864 --background_color 'white' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
865 --dpi '80' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
866 --x_width '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
867 --y_height '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
868 --bar_width '0.75' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
869 --type_of_file 'png' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
870 --chart_type 'area,bar,pie' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
871 --resize_nth_label '0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
872 --label_type 'categorical' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
873 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
874 plot_taxa_summary.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
875 --counts_fname 'test-data/plot_taxa_summary/phylum.txt,test-data/plot_taxa_summary/class.txt,test-data/plot_taxa_summary/genus.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
876 --dir_path 'test-data/plot_taxa_summary/phylum_class_genus' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
877 --labels 'Phylum,Class,Genus' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
878 --num_categories '20' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
879 --background_color 'white' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
880 --dpi '80' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
881 --x_width '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
882 --y_height '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
883 --bar_width '0.75' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
884 --type_of_file 'png' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
885 --chart_type 'area,bar,pie' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
886 --resize_nth_label '0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
887 --label_type 'categorical' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
888 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
889 plot_taxa_summary.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
890 --counts_fname 'test-data/plot_taxa_summary/class.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
891 --dir_path 'test-data/plot_taxa_summary/class' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
892 --labels 'Class' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
893 --num_categories '10' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
894 --background_color 'white' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
895 --dpi '80' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
896 --x_width '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
897 --y_height '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
898 --bar_width '0.75' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
899 --chart_type 'pie' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
900 --type_of_file 'svg' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
901 --include_html_legend \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
902 --resize_nth_label '0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
903 --label_type 'categorical' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
904 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
905 plot_taxa_summary.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
906 --counts_fname 'test-data/plot_taxa_summary/class.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
907 --dir_path 'test-data/plot_taxa_summary/class_colorby' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
908 --labels 'Class' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
909 --num_categories '20' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
910 --colorby 'PC.636,PC.635' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
911 --background_color 'white' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
912 --dpi '80' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
913 --x_width '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
914 --y_height '12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
915 --bar_width '0.75' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
916 --type_of_file 'pdf' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
917 --chart_type 'area,bar,pie' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
918 --resize_nth_label '0' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
919 --label_type 'categorical' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
920 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
921 # split_libraries |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
922 split_libraries.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
923 --map 'test-data/split_libraries/mapping_file.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
924 -o split_libraries \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
925 --fasta 'test-data/split_libraries/reads_1.fna,test-data/split_libraries/reads_2.fna' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
926 --qual 'test-data/split_libraries/reads_1.qual,test-data/split_libraries/reads_2.qual' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
927 --min_qual_score 25 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
928 --qual_score_window 0 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
929 --record_qual_scores \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
930 --min_seq_length 200 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
931 --max_seq_length 1000 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
932 --max_ambig 6 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
933 --max_homopolymer 6 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
934 --max_primer_mismatch 0 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
935 --barcode_type 'golay_12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
936 --max_barcode_errors 1.5 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
937 --start_numbering_at 1 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
938 cp split_libraries/seqs.fna 'test-data/split_libraries/seqs.fna' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
939 cp split_libraries/split_library_log.txt 'test-data/split_libraries/split_library_log' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
940 cp split_libraries/histograms.txt 'test-data/split_libraries/histograms.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
941 cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
942 rm -rf split_libraries |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
943 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
944 # split_libraries_fastq |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
945 split_libraries_fastq.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
946 --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
947 -o split_libraries \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
948 --mapping_fps 'test-data/map.tsv' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
949 --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
950 --store_qual_scores \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
951 --store_demultiplexed_fastq \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
952 --max_bad_run_length 3 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
953 --min_per_read_length_fraction 0.75 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
954 --sequence_max_n 0 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
955 --start_seq_id 0 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
956 --barcode_type 'golay_12' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
957 --max_barcode_errors 1.5 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
958 cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
959 cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
960 cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
961 cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
962 rm -rf split_libraries |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
963 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
964 # summarize_taxa |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
965 cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
966 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
967 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
968 summarize_taxa.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
969 -i 'test-data/summarize_taxa/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
970 -o summarize_taxa_1 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
971 -L '2,3,4,5,6' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
972 -m 'test-data/summarize_taxa/map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
973 --md_identifier "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
974 --delimiter ";" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
975 cp summarize_taxa_1/*_L2.txt "test-data/summarize_taxa/1_L2.txt" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
976 cp summarize_taxa_1/*_L3.txt "test-data/summarize_taxa/1_L3.txt" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
977 cp summarize_taxa_1/*_L4.txt "test-data/summarize_taxa/1_L4.txt" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
978 cp summarize_taxa_1/*_L5.txt "test-data/summarize_taxa/1_L5.txt" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
979 cp summarize_taxa_1/*_L6.txt "test-data/summarize_taxa/1_L6.txt" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
980 rm -rf summarize_taxa_1 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
981 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
982 summarize_taxa.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
983 -i 'test-data/summarize_taxa/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
984 -o summarize_taxa_2 \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
985 -L '3,6' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
986 --md_identifier "taxonomy" \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
987 --delimiter ";" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
988 cp summarize_taxa_2/*_L3.txt "test-data/summarize_taxa/2_L3.txt" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
989 cp summarize_taxa_2/*_L6.txt "test-data/summarize_taxa/2_L6.txt" |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
990 rm -rf summarize_taxa_2 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
991 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
992 # summarize_taxa_through_plots |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
993 summarize_taxa_through_plots.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
994 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
995 --output_dir summarize_taxa_through_plots_mapping \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
996 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
997 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
998 -i 'summarize_taxa_through_plots_mapping/otu_table_L2.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
999 -o 'summarize_taxa_through_plots_mapping/otu_table_L2_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1000 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1001 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1002 -i 'summarize_taxa_through_plots_mapping/otu_table_L3.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1003 -o 'summarize_taxa_through_plots_mapping/otu_table_L3_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1004 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1005 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1006 -i 'summarize_taxa_through_plots_mapping/otu_table_L4.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1007 -o 'summarize_taxa_through_plots_mapping/otu_table_L4_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1008 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1009 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1010 -i 'summarize_taxa_through_plots_mapping/otu_table_L5.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1011 -o 'summarize_taxa_through_plots_mapping/otu_table_L5_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1012 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1013 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1014 -i 'summarize_taxa_through_plots_mapping/otu_table_L6.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1015 -o 'summarize_taxa_through_plots_mapping/otu_table_L6_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1016 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1017 cp summarize_taxa_through_plots_mapping/*.txt test-data/summarize_taxa_through_plots/mapping/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1018 cp summarize_taxa_through_plots_mapping/*_json.biom test-data/summarize_taxa_through_plots/mapping/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1019 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping/area_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1020 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping/bar_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1021 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1022 summarize_taxa_through_plots.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1023 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1024 --output_dir summarize_taxa_through_plots_mapping_categories \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1025 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1026 --mapping_category 'Treatment' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1027 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1028 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1029 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1030 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1031 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1032 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1033 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1034 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1035 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1036 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1037 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1038 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1039 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1040 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1041 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1042 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1043 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1044 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1045 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1046 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1047 cp summarize_taxa_through_plots_mapping_categories/*.txt test-data/summarize_taxa_through_plots/mapping_categories/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1048 cp summarize_taxa_through_plots_mapping_categories/*_json.biom test-data/summarize_taxa_through_plots/mapping_categories/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1049 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1050 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1051 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1052 summarize_taxa_through_plots.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1053 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1054 --output_dir summarize_taxa_through_plots_mapping_sort \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1055 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1056 --sort |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1057 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1058 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1059 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1060 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1061 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1062 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1063 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1064 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1065 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1066 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1067 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1068 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1069 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1070 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1071 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1072 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1073 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1074 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1075 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1076 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1077 cp summarize_taxa_through_plots_mapping_sort/*.txt test-data/summarize_taxa_through_plots/mapping_sort/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1078 cp summarize_taxa_through_plots_mapping_sort/*_json.biom test-data/summarize_taxa_through_plots/mapping_sort/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1079 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1080 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1081 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1082 summarize_taxa_through_plots.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1083 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1084 --output_dir summarize_taxa_through_plots_without_mapping |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1085 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1086 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L2.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1087 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L2_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1088 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1089 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1090 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L3.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1091 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L3_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1092 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1093 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1094 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L4.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1095 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L4_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1096 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1097 biom convert \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1098 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L5.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1099 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L5_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1100 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1101 biom convert \ |
f9df45b8425a
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_without_mapping/otu_table_L6.biom' \ |
f9df45b8425a
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_without_mapping/otu_table_L6_json.biom' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1104 --to-json |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1105 cp summarize_taxa_through_plots_without_mapping/*.txt test-data/summarize_taxa_through_plots/without_mapping/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1106 cp summarize_taxa_through_plots_without_mapping/*_json.biom test-data/summarize_taxa_through_plots/without_mapping/ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1107 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/area_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1108 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1109 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1110 # upgma_cluster |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1111 upgma_cluster.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1112 --input_path 'test-data/upgma_cluster/' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1113 --output_path 'test-data/upgma_cluster/' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1114 |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1115 # validate_mapping_file |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1116 validate_mapping_file.py \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1117 -m 'test-data/validate_mapping_file/map.tsv' \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1118 -o validate_mapping_file_output \ |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1119 -c '_' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1120 cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1121 cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1122 cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt' |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
1123 rm -rf validate_mapping_file_output |