Mercurial > repos > iuc > qiime_alpha_diversity

comparison generate_test_data.sh @ 3:fdd0a0d19b5c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
author iuc
date Thu, 22 Jun 2017 06:59:25 -0400
parents 2ceee245d97c
children ffe438e1fc67
comparison
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2:44030fc533cc 3:fdd0a0d19b5c
90 --assignment_method 'uclust' \ 90 --assignment_method 'uclust' \
91 --min_consensus_fraction '0.51' \ 91 --min_consensus_fraction '0.51' \
92 --similarity '0.9' \ 92 --similarity '0.9' \
93 --uclust_max_accepts '3' \ 93 --uclust_max_accepts '3' \
94 -o assign_taxonomy_uclust 94 -o assign_taxonomy_uclust
95 cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt 'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt' 95 ls assign_taxonomy_uclust
96 md5sum 'assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt'
96 rm -rf assign_taxonomy_uclust 97 rm -rf assign_taxonomy_uclust
98
99 assign_taxonomy.py \
100 --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \
101 --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \
102 --assignment_method 'mothur' \
103 --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
104 --confidence '0.5' \
105 -o assign_taxonomy_mothur
106 ls assign_taxonomy_mothur
107 md5sum 'assign_taxonomy_mothur/mothur_repr_set_seqs_tax_assignments.txt'
108 rm -rf assign_taxonomy_mothur
109
110 assign_taxonomy.py \
111 --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \
112 --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \
113 --assignment_method 'mothur' \
114 --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
115 --blast_e_value '0.001' \
116 -o assign_taxonomy_blast
117 ls assign_taxonomy_blast
118 md5sum 'assign_taxonomy_blast/mothur_repr_set_seqs_tax_assignments.txt'
119 rm -rf assign_taxonomy_blast
97 120
98 #assign_taxonomy.py \ 121 #assign_taxonomy.py \
99 # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \ 122 # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \
100 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \ 123 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \
101 # --assignment_method 'rdp' \ 124 # --assignment_method 'rdp' \
114 # --amplicon_id_regex "(\S+)\s+(\S+?)\/" \ 137 # --amplicon_id_regex "(\S+)\s+(\S+?)\/" \
115 # --header_id_regex "\S+\s+(\S+?)\/" \ 138 # --header_id_regex "\S+\s+(\S+?)\/" \
116 # -o assign_taxonomy_rtax 139 # -o assign_taxonomy_rtax
117 #ls assign_taxonomy_rtax 140 #ls assign_taxonomy_rtax
118 141
119 #assign_taxonomy.py \
120 # --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
121 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \
122 # --assignment_method 'mothur' \
123 # --confidence 0.5 \
124 # -o assign_taxonomy_mothur
125 #ls assign_taxonomy_mothur
126
127 assign_taxonomy.py \ 142 assign_taxonomy.py \
128 --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ 143 --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
129 --assignment_method 'sortmerna' \ 144 --assignment_method 'sortmerna' \
130 --min_consensus_fraction "0.51" \ 145 --min_consensus_fraction "0.51" \
131 --similarity "0.9" \ 146 --similarity "0.9" \
132 --sortmerna_e_value "1.0" \ 147 --sortmerna_e_value "1.0" \
133 --sortmerna_coverage "0.9" \ 148 --sortmerna_coverage "0.9" \
134 --sortmerna_best_N_alignments "5" \ 149 --sortmerna_best_N_alignments "5" \
135 -o assign_taxonomy_sortmerna 150 -o assign_taxonomy_sortmerna
136 cp assign_taxonomy_sortmerna/sortmerna_map.blast 'test-data/assign_taxonomy/sortmerna_map.blast' 151 ls assign_taxonomy_sortmerna
137 cp assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt 'test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt' 152 md5sum 'assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt'
153 md5sum 'assign_taxonomy_sortmerna/sortmerna_map.blast'
138 rm -rf assign_taxonomy_sortmerna 154 rm -rf assign_taxonomy_sortmerna
139 155
140 #beta_diversity 156 #beta_diversity
141 beta_diversity.py \ 157 beta_diversity.py \
142 --input_path 'test-data/beta_diversity/otu_table.biom' \ 158 --input_path 'test-data/beta_diversity/otu_table.biom' \
1103 -c '_' 1119 -c '_'
1104 cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html' 1120 cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html'
1105 cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log' 1121 cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log'
1106 cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt' 1122 cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt'
1107 rm -rf validate_mapping_file_output 1123 rm -rf validate_mapping_file_output
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