Mercurial > repos > iuc > qiime_summarize_taxa

annotate jackknifed_beta_diversity_output_management.py @ 5:50df54a9ae82 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:19:08 -0400
parents 2f2e4388bd05
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
1 #!/usr/bin/env python
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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2 # -*- coding: utf-8 -*-
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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3
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iuc
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4 import argparse
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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5 import os
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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6
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7
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iuc
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8 def generate_index_html(dir_list, args):
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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9 with open(args.html_file, 'w') as index_html_file:
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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10 s = '<html>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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11 s += '\t<head>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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12 s += '\t\t<title>Jackknifed beta diversity results</title>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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13 s += '\t</head>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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14 s += '\t<body>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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15 s += '\t\t<a href="http://www.qiime.org" target="_blank">'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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16 s += '<img src="http://qiime.org/_static/wordpressheader.png"'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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17 s += 'alt="www.qiime.org""/></a>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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18 s += '\t\t<p>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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19 s += '\t\t\tEmperor PCoA plot after jacknifed beta diversity\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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20 s += '\t\t\t<ul>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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21
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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22 for directory in dir_list:
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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23 if directory == 'rarefaction' or directory == 'unrarefied_bdiv':
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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24 continue
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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25
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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26 s += '\t\t\t\t<li><a href="' + directory
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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27 s += '/index.html">PCoA plots</a></td></li>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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iuc
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29 s += '\t\t\t</ul>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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30 s += '\t\t</p>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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31 s += '\t</body>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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32 s += '</html>\n'
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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33 index_html_file.write(s)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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iuc
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36 def build_html(args):
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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37 os.mkdir(args.html_dir)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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38
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iuc
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39 dir_list = [name for name in os.listdir(args.data_directory)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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40 if os.path.isdir(os.path.join(
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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41 args.data_directory,
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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42 name))]
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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43
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iuc
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44 generate_index_html(dir_list, args)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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45
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46 os.mkdir(args.data_directory + '/pcoa')
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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47 os.mkdir(args.data_directory + '/rare_dm')
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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48 os.mkdir(args.data_directory + '/rare_upgma')
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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49 os.mkdir(args.data_directory + '/upgma_cmp')
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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50 os.mkdir(args.data_directory + '/rare_upgma_consensus')
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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51
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52 for directory in dir_list:
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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53 if directory == 'rarefaction' or directory == 'unrarefied_bdiv':
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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54 continue
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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55
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56 input_dir = os.path.join(args.data_directory, directory)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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57
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58 input_path = os.path.join(input_dir, "emperor_pcoa_plots")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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59 output_path = os.path.join(args.html_dir, directory)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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60 cmd = 'cp -r ' + input_path + ' ' + output_path
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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61 os.system(cmd)
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62
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63 input_path = os.path.join(input_dir, "pcoa/*")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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64 output_path = os.path.join(args.data_directory, "pcoa")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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65 cmd = 'cp -r ' + input_path + ' ' + output_path
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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66 os.system(cmd)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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67
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68 input_path = os.path.join(input_dir, "rare_dm/*")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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69 output_path = os.path.join(args.data_directory, "rare_dm")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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70 cmd = 'cp -r ' + input_path + ' ' + output_path
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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71 os.system(cmd)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72
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73 input_path = os.path.join(input_dir, "rare_upgma/*")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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74 output_path = os.path.join(args.data_directory, "rare_upgma")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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75 cmd = 'cp -r ' + input_path + ' ' + output_path
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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76 os.system(cmd)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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77
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iuc
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78 input_path = os.path.join(input_dir, "upgma_cmp/*")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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79 output_path = os.path.join(args.data_directory, "upgma_cmp")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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80 cmd = 'cp -r ' + input_path + ' ' + output_path
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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81 os.system(cmd)
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82
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iuc
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83 input_path = os.path.join(input_dir, "rare_upgma_consensus.tre")
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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84 output_path = os.path.join(
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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85 args.data_directory,
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86 "rare_upgma_consensus",
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87 directory + '.tre')
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88 cmd = 'cp ' + input_path + ' ' + output_path
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89 os.system(cmd)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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90
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91
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92 if __name__ == '__main__':
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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93 parser = argparse.ArgumentParser()
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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94 parser.add_argument('--data_directory', required=True)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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95 parser.add_argument('--html_file', required=True)
2f2e4388bd05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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96 parser.add_argument('--html_dir', required=True)
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97 args = parser.parse_args()
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98
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99 build_html(args)