# HG changeset patch
# User iuc
# Date 1498129074 14400
# Node ID ec3c4654eacc201dc700a7dbf0ac8df6d05d68b4
# Parent 70206002b220affadc483ad053c59033b9953c07
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
diff -r 70206002b220 -r ec3c4654eacc assign_taxonomy.xml
--- a/assign_taxonomy.xml Fri May 19 04:09:30 2017 -0400
+++ b/assign_taxonomy.xml Thu Jun 22 06:57:54 2017 -0400
@@ -4,7 +4,7 @@
macros.xml
- rdptools
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blast-legacy
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mothur
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+ methodcond['assignment_method']!="mothur"
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methodcond['assignment_method']=="sortmerna"
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diff -r 70206002b220 -r ec3c4654eacc test-data/assign_taxonomy/mothur_id_to_taxonomy.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/mothur_id_to_taxonomy.txt Thu Jun 22 06:57:54 2017 -0400
@@ -0,0 +1,7 @@
+X67228 Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium
+X73443 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium
+AB004750 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter
+xxxxxx Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas
+AB004748 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter
+AB000278 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Photobacterium
+AB000390 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Vibrio
diff -r 70206002b220 -r ec3c4654eacc test-data/assign_taxonomy/mothur_repr_set_seqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/mothur_repr_set_seqs.fasta Thu Jun 22 06:57:54 2017 -0400
@@ -0,0 +1,4 @@
+>X67228 some description
+aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa
+>EF503697
+TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC
diff -r 70206002b220 -r ec3c4654eacc test-data/assign_taxonomy/sortmerna_input_seqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/sortmerna_input_seqs.fasta Thu Jun 22 06:57:54 2017 -0400
@@ -0,0 +1,2 @@
+>X67228
+aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa
diff -r 70206002b220 -r ec3c4654eacc test-data/assign_taxonomy/sortmerna_map.blast
--- a/test-data/assign_taxonomy/sortmerna_map.blast Fri May 19 04:09:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-X67228 152350 98.6 277 4 0 1 277 22 298 5.76e-129 464 277M 100
-X67228 558499 97.1 275 8 0 1 275 2 276 1.05e-122 443 275M2S 99.3
-X67228 553706 97.5 277 7 0 1 277 1 277 4.7e-125 451 277M 100
-X67228 553981 95.7 277 12 0 1 277 2 278 1.55e-118 429 277M 100
-X67228 4423084 98.6 277 4 0 1 277 21 297 5.76e-129 464 277M 100
-X73443 179865 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D20M1I26M1I115M1D54M 97.5
-X73443 181718 96 269 3 8 8 276 2 268 4.66e-113 411 7S3M1I28M1I3M1I7M1D8M1D20M1I26M1I115M1D54M 97.5
-X73443 193551 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5
-X73443 212341 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5
-X73443 175883 96 269 3 8 8 276 2 268 4.66e-113 411 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5
-AB004750 3888577 100 339 0 0 1 339 26 364 1.61e-166 588 339M 100
-AB004750 581782 97.6 339 8 0 1 339 27 365 4.36e-156 554 339M 100
-AB004750 1108679 97.9 339 7 0 1 339 26 364 2.16e-157 558 339M 100
-AB004750 1109844 97.9 339 7 0 1 339 26 364 2.16e-157 558 339M 100
-AB004750 4418165 99.7 339 1 0 1 339 28 366 3.25e-165 584 339M 100
-xxxxxx 1102995 97.5 361 8 1 1 361 22 383 2.94e-166 588 174M1D187M 100
-xxxxxx 340031 95.6 361 13 3 1 361 23 386 1.07e-158 562 169M3D192M 100
-xxxxxx 340031 95.6 361 13 3 1 361 23 386 1.07e-158 562 169M3D192M 100
-AB004748 581782 98 396 8 0 1 396 27 422 8.13e-186 653 396M 100
-AB004748 1108679 98.2 396 7 0 1 396 26 421 4.04e-187 657 396M 100
-AB004748 1109844 98.2 396 7 0 1 396 26 421 4.04e-187 657 396M 100
-AB004748 3888577 100 396 0 0 1 396 26 421 3.01e-196 687 396M 100
-AB004748 561327 97.5 396 10 0 1 396 1 396 3.3e-183 644 396M 100
-AB000278 554346 98.6 368 5 0 1 368 6 373 4e-175 617 368M 100
-AB000278 160928 97 368 7 4 1 368 33 400 2.94e-166 588 33M1D5M1I8M1I2M1D318M 100
-AB000390 4433053 98.1 317 6 0 1 317 13 329 3.2e-147 524 317M 100
-AB000390 19456 94.4 317 14 4 1 317 12 328 4.28e-132 474 77M2D4M2I234M 100
-AB000390 4432126 94.4 317 14 4 1 317 13 329 4.28e-132 474 77M2D4M2I234M 100
diff -r 70206002b220 -r ec3c4654eacc test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt
--- a/test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt Fri May 19 04:09:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-#OTU ID taxonomy confidence num hits
-AB004750 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__ 0.60 5
-AB000390 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Vibrionales; f__Vibrionaceae 1.00 3
-xxxxxx k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Alteromonadales; f__Alteromonadaceae; g__Marinobacter; s__ 1.00 3
-X67228 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Rhizobiaceae 0.60 5
-AB000278 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Vibrionales; f__Vibrionaceae; g__Photobacterium 1.00 2
-AB004748 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__ 0.60 5
-X73443 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae 1.00 5
diff -r 70206002b220 -r ec3c4654eacc test-data/assign_taxonomy/uclust_taxonomic_assignation.txt
--- a/test-data/assign_taxonomy/uclust_taxonomic_assignation.txt Fri May 19 04:09:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-11469739 k__Bacteria; p__OP9; c__JS1; o__SB-45; f__; g__; s__ 1.00 3
-11480235 k__Bacteria; p__OD1; c__; o__; f__; g__; s__ 1.00 1
-11460543 k__Bacteria; p__OP9; c__JS1; o__SB-45; f__; g__; s__ 1.00 3
-11460523 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfobacterales; f__Desulfobulbaceae; g__; s__ 1.00 3
-11472286 k__Bacteria; p__WS5; c__; o__; f__; g__; s__ 1.00 1
-11458037 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Peptococcaceae; g__Desulfosporosinus; s__meridiei 1.00 3
-11472384 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Burkholderia; s__ 0.67 3
-11469752 k__Bacteria; p__TM7; c__TM7-1; o__; f__; g__; s__ 1.00 3
-11480408 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 1.00 3
-11468680 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Burkholderia; s__ 1.00 3