# HG changeset patch
# User iuc
# Date 1521598506 14400
# Node ID a037860aad0bf97edf68918a8dd6deba142bad6a
# Parent 90fc3380e69060dcbf6572eb70f4af5bad6d992f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
diff -r 90fc3380e690 -r a037860aad0b chimera.pintail.xml
--- a/chimera.pintail.xml Tue Sep 05 16:54:46 2017 -0400
+++ b/chimera.pintail.xml Tue Mar 20 22:15:06 2018 -0400
@@ -7,83 +7,90 @@
0:
- window=$window,
- #end if
- #if int($increment) > 0:
- increment=$increment,
- #end if
- processors='\${GALAXY_SLOTS:-8}'
- )'
- | sed 's/ //g' ## mothur trips over whitespace
- | mothur
- | tee mothur.out.log
+echo 'chimera.pintail(
+ fasta=fasta.dat,
+ reference=alignment.reference.dat,
+ filter=$filter,
+ #if $mask_cond.source2 == "default":
+ mask=default,
+ #elif $mask_cond.source2 == "history":
+ mask=mask.dat,
+ #end if
+ #if $conservation:
+ conservation=conservation.dat,
+ #end if
+ #if $quantile:
+ quantile=quantile.dat,
+ #end if
+ #if int($window) > 0:
+ window=$window,
+ #end if
+ #if int($increment) > 0:
+ increment=$increment,
+ #end if
+ processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g' ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
]]>
-
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conservation == None
@@ -94,32 +101,33 @@
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+ ]]>
10.1128/AEM.71.12.7724-7736.2005
diff -r 90fc3380e690 -r a037860aad0b macros.xml
--- a/macros.xml Tue Sep 05 16:54:46 2017 -0400
+++ b/macros.xml Tue Mar 20 22:15:06 2018 -0400
@@ -1,11 +1,13 @@
+ 1.39.5
- mothur
+ mothur
+
- mothur "#help()" | sed '7q;d' | cut -d" " -f2
+
@@ -13,20 +15,10 @@
- 1.36.1
set -o pipefail;
-
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@@ -78,9 +70,70 @@
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10.1128/AEM.01541-09
diff -r 90fc3380e690 -r a037860aad0b test-data/Fasting_Example1.scrap.sff
Binary file test-data/Fasting_Example1.scrap.sff has changed
diff -r 90fc3380e690 -r a037860aad0b test-data/amazon.an.0.03.pearson.otu.corr
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.0.03.pearson.otu.corr Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,3829 @@
+OTUA OTUB pearsonCoef Significance
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+Otu06 Otu01 1.000000 0.000000
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+Otu07 Otu05 -nan 0.000000
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diff -r 90fc3380e690 -r a037860aad0b test-data/amazon.otus.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.otus.accnos Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,3 @@
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diff -r 90fc3380e690 -r a037860aad0b test-data/esophagus.fn.shared
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/esophagus.fn.shared Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,12 @@
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+0.10 C 58 19 41 42 41 2 10 7 1 0 0 2 0 5 13 4 0 0 1 0 6 0 2 14 0 0 7 0 0 4 2 2 2 4 3 1 8 4 1 1 1 1 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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diff -r 90fc3380e690 -r a037860aad0b test-data/samplebiom.biom1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplebiom.biom1 Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,8668 @@
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+ "format_url": "http://biom-format.org",
+ "type": "OTU table",
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+ [3985,0,1],
+ [3986,0,1]]
+}
diff -r 90fc3380e690 -r a037860aad0b test-data/stool_small.count_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.count_table Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,47 @@
+Representative_Sequence total
+F11Fcsw_12747 1
+F11Fcsw_13125 1
+F11Fcsw_13572 2
+F11Fcsw_13584 1
+F11Fcsw_13612 2
+F11Fcsw_13784 2
+F11Fcsw_14513 1
+F11Fcsw_14920 1
+F11Fcsw_14954 1
+F11Fcsw_14980 1
+F11Fcsw_15042 1
+F11Fcsw_15664 1
+F11Fcsw_17394 1
+F11Fcsw_17898 1
+F11Fcsw_18564 1
+F11Fcsw_19115 1
+F11Fcsw_19402 1
+F11Fcsw_19500 1
+F11Fcsw_20028 1
+F11Fcsw_20361 1
+F11Fcsw_20429 1
+F11Fcsw_20462 1
+F11Fcsw_20686 1
+F11Fcsw_21035 1
+F11Fcsw_21196 1
+F11Fcsw_21505 1
+F11Fcsw_21636 1
+F11Fcsw_21645 1
+F11Fcsw_21954 1
+F11Fcsw_22687 1
+F11Fcsw_22831 1
+F11Fcsw_22880 1
+F11Fcsw_22900 1
+F11Fcsw_23043 1
+F11Fcsw_23322 1
+F11Fcsw_23608 1
+F11Fcsw_23684 1
+F11Fcsw_24087 1
+F11Fcsw_24273 1
+F11Fcsw_24701 2
+F11Fcsw_24967 1
+F11Fcsw_25501 1
+F11Fcsw_25574 1
+F11Fcsw_26078 1
+F11Fcsw_26175 1
+F11Fcsw_26418 1
diff -r 90fc3380e690 -r a037860aad0b test-data/stool_small.denovo.vsearch.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.denovo.vsearch.accnos Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,2 @@
+F11Fcsw_21505
+F11Fcsw_23322
diff -r 90fc3380e690 -r a037860aad0b test-data/stool_small.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.names Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,46 @@
+F11Fcsw_12747 F11Fcsw_12747
+F11Fcsw_13125 F11Fcsw_13125
+F11Fcsw_13572 F11Fcsw_13572,F11Fcsw_14202
+F11Fcsw_13584 F11Fcsw_13584
+F11Fcsw_13612 F11Fcsw_13612,F11Fcsw_23132
+F11Fcsw_13784 F11Fcsw_13784,F11Fcsw_21715
+F11Fcsw_14513 F11Fcsw_14513
+F11Fcsw_14920 F11Fcsw_14920
+F11Fcsw_14954 F11Fcsw_14954
+F11Fcsw_14980 F11Fcsw_14980
+F11Fcsw_15042 F11Fcsw_15042
+F11Fcsw_15664 F11Fcsw_15664
+F11Fcsw_17394 F11Fcsw_17394
+F11Fcsw_17898 F11Fcsw_17898
+F11Fcsw_18564 F11Fcsw_18564
+F11Fcsw_19115 F11Fcsw_19115
+F11Fcsw_19402 F11Fcsw_19402
+F11Fcsw_19500 F11Fcsw_19500
+F11Fcsw_20028 F11Fcsw_20028
+F11Fcsw_20361 F11Fcsw_20361
+F11Fcsw_20429 F11Fcsw_20429
+F11Fcsw_20462 F11Fcsw_20462
+F11Fcsw_20686 F11Fcsw_20686
+F11Fcsw_21035 F11Fcsw_21035
+F11Fcsw_21196 F11Fcsw_21196
+F11Fcsw_21505 F11Fcsw_21505
+F11Fcsw_21636 F11Fcsw_21636
+F11Fcsw_21645 F11Fcsw_21645
+F11Fcsw_21954 F11Fcsw_21954
+F11Fcsw_22687 F11Fcsw_22687
+F11Fcsw_22831 F11Fcsw_22831
+F11Fcsw_22880 F11Fcsw_22880
+F11Fcsw_22900 F11Fcsw_22900
+F11Fcsw_23043 F11Fcsw_23043
+F11Fcsw_23322 F11Fcsw_23322
+F11Fcsw_23608 F11Fcsw_23608
+F11Fcsw_23684 F11Fcsw_23684
+F11Fcsw_24087 F11Fcsw_24087
+F11Fcsw_24273 F11Fcsw_24273
+F11Fcsw_24701 F11Fcsw_24701,F11Fcsw_24794
+F11Fcsw_24967 F11Fcsw_24967
+F11Fcsw_25501 F11Fcsw_25501
+F11Fcsw_25574 F11Fcsw_25574
+F11Fcsw_26078 F11Fcsw_26078
+F11Fcsw_26175 F11Fcsw_26175
+F11Fcsw_26418 F11Fcsw_26418
diff -r 90fc3380e690 -r a037860aad0b test-data/stool_small.unique.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.unique.fasta Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,92 @@
+>F11Fcsw_12747
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGCAGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATCAGATATGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATCCCAGAGATGCCTCCAAAATACATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGG
+>F11Fcsw_13125
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGACCCATCGTAAAGCGATAGCTTACAAGTAGAGGCCATCTTTAGTCGAGCTTCCATGCGGAAGTTCGACAACATTCGGTATTAGCAGTCCTTTCGAACTGTTGTCCCCATCTTTACGG
+>F11Fcsw_13572
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAAA
+>F11Fcsw_13584
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGATGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGGTTATCGAAATTCTTTAATAACAAGAAGATGCCTTCTCGTTATACTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCGGAATAACCGGTAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAACCTA
+>F11Fcsw_13612
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATGCGCCGCATGCCCATCCCTGTCCGGATTACTCCTTTGGCGCTCGCAGGATGCCCCGCAAACGCTTTATGCGATATTAGACCGGATTTCTCCGGATTATCCCTCTGACAGGGGCAGGTTGCATACGTGTTACTCACCCG
+>F11Fcsw_13784
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG
+>F11Fcsw_14513
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGATCACCCTCTCAGGTCGGCTAACCATCGTCGACTTGGTAGTCCGTTACACTACCAACTATCTAATGGTACGCGAGCCCATCCACATCCGATAAATCTTTTACCCCTGAGAGATGCCTCTCTGTGGTCTTATGCGGTATTAGCACACATTTCTATGTGTTATTCCCCAGATGTGGGCAGGTTG
+>F11Fcsw_14920
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTGAGCCATTACCTCTCCAACTAGCTAATCAGACGCGGGCCCATCCTATACCACCTGAGTTTTTCCTACCGTATCATGCGGTACTGTAGGCTTATGCGGTTTTAGCACAGATTTCTCTGTGTTATCCCCTGTATAGGGCAGGTTACCCACGCGTTT
+>F11Fcsw_14954
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCGGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATGTCCGGGATGCCCCGGTCATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACGCGTTACT
+>F11Fcsw_14980
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTTTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGATCGGCTACCCATCGTCGCCTTGGTGAGCCGTTACCTCTCCAACTAGCTAATGGGCCGCGAGCCCCTCCTATACCGCCTCAGCTTTTACCCCTCTCCGATGCCGGAGTGTGGTCTTATACCGTATTAGCACAAATTTCTCTGTGTTATCCCGTTGTATAGGATAGGTTGCTCACGTGTTACTCACCCG
+>F11Fcsw_15042
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCGTTTCCAGCTGTTATCCCCCGGTATGGGGCAGGTCACCCACGCGTTACT
+>F11Fcsw_15664
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTACT
+>F11Fcsw_17394
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTAGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTCACACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTATTATCAGCCGTTTCCAACTGCTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTA
+>F11Fcsw_17898
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGTATCATGCGATACCGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCGTTACTCACCCG
+>F11Fcsw_18564
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGG
+>F11Fcsw_19115
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGCCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAGGTTATCCCCAACGTGGTGGGCGAGGTTGGATACGCGTTACTCACCCGTCCCG
+>F11Fcsw_19402
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCTGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATTGCCAAACGATGCCGTTCGGCAATGTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCACTGAAAGGTAGGTTG
+>F11Fcsw_19500
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGAGGCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG
+>F11Fcsw_20028
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTATGGGCCGTGTCTCAGTCCCATTGTGGCTGATCATCCTCTCAAACCAGCTACTGATCGTCGCCTTGGTAGTCCATTACACCACCAACAAGCTAATCAGGTGCAGGCTCATCCTAGAGCACCGGAGTTTTCAAGATTGGTATTTCAACCAAGCTCATATGGGGTATTAGCAGAAGTTTCCTTCTGTTGTCCCCCTCTCTAGGGCAGATTT
+>F11Fcsw_20361
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGTCCGTGTCTCAGTACCAGTGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTTGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATACAACGCATGTCCATCTATAACCACCGGAGTTTTCAACCCGGAGAGATGCCTCTCCGAATATTATGGGGAATTAGTACCAATTTCTCAGTGTTATGCCCCTGTTATAGGTAGGTTACATACGCGTTACGCACCCGTGCGCCGG
+>F11Fcsw_20429
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAAAAATATCATGCGATATTCGTATGCTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>F11Fcsw_20462
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTATGGGCCGTGTCTCAGTCCCATTGTGGCTGATCATCCTCTCAAACCAGCTACTGATCGTCGCCTTGGTAGTCCATTACACCACCAACAAGCTAATCAGGTGCAGGCTCATCCTAGAGCACCGGAGTTTTCAAGATTGGTATTTCAACCAAGCTCATATGGGGTATTAGCAGAAGTTTCCTTCTGTTGTCCCCCTCTCTAGGGCAGATTTT
+>F11Fcsw_20686
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACGGAACCATGCGGTTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGGCTGTTATCCCCCTCTGAAAGGCAGGTTGCTCACGCG
+>F11Fcsw_21035
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGGCTTGGTGAGCCGTTACCTCACCAACTACCTAATCAGACGCGAGTCCATCTGCAAGCGGTTTCCCTTTGGCATCATCTCCATGCGGAATCGATGCGTTATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTCGCAGGCAGGTTACT
+>F11Fcsw_21196
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGGCTTGGTGGGCTGTTATCTCACCAACTACCTAATCGGCCGCGAGCCCATCTCTCAGCGATAAAATCTTTGATAGTCTCCGGATGCCCGGAAACTATGTTATGCGGTATTAGCGTTCGTTTCCAAACGTTATTCCACTCTGAAAGGCAGGTTACTCACGTGTTACT
+>F11Fcsw_21505
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATCCACGCGTTACTCACCCGTCCGCCACTCAGT
+>F11Fcsw_21636
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCATCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGGCCCATCCTCTAGCGATAGCTTATAAATAGAGGCCATCTTTCACAGCATCCTCATGCGAGATTGCTGTCACATTCGGTATTAGCACCCTTCGGA
+>F11Fcsw_21645
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAATTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCG
+>F11Fcsw_21954
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAA
+>F11Fcsw_22687
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTTGCCTTGGTGGGCCATTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAGGTTATCCCAACGTGGTGGGCGAGGTTGGATACGCGTTACTCACCCG
+>F11Fcsw_22831
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT
+>F11Fcsw_22880
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCCCACCAACTAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCG
+>F11Fcsw_22900
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATTCACGCGTTACTCACCCG
+>F11Fcsw_23043
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTA
+>F11Fcsw_23322
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCCGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCGCCAA
+>F11Fcsw_23608
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTAGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCG
+>F11Fcsw_23684
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCCCTTTCAGATGTCTTCTAGAGACGTCATTGGGTATTAGTCTTACTTTCGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCGTGCG
+>F11Fcsw_24087
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACAAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACG
+>F11Fcsw_24273
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCAGACGCGAGCCCATCTATCAGCGGATTACTCCTTTCCCACTTTCATCATGTGATATTTATTGGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCCTGATAGGCG
+>F11Fcsw_24701
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCG
+>F11Fcsw_24967
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT
+>F11Fcsw_25501
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATTTCGACCATGCGATCAAAATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACG
+>F11Fcsw_25574
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGAAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG
+>F11Fcsw_26078
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTATCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCA
+>F11Fcsw_26175
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG
+>F11Fcsw_26418
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACT
diff -r 90fc3380e690 -r a037860aad0b test-data/stool_small.vsearch.chimeras
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.vsearch.chimeras Tue Mar 20 22:15:06 2018 -0400
@@ -0,0 +1,47 @@
+Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN
+0.0000 F11Fcsw_13572;size=2; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_13612;size=2; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_13784;size=2; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_24701;size=2; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_12747;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0514 F11Fcsw_13125;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 80.5 77.1 80.1 72.7 80.1 21 20 19 8 0 6 0.4 N
+0.1560 F11Fcsw_13584;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 82.5 80.4 72.9 73.3 80.4 23 0 8 15 10 24 2.1 N
+0.0259 F11Fcsw_14513;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.7 79.3 81.4 81.9 81.4 11 8 11 11 3 19 1.3 N
+0.0550 F11Fcsw_14920;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.7 83.5 76.3 80.9 83.5 23 3 21 5 2 10 1.3 N
+0.0000 F11Fcsw_14954;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0216 F11Fcsw_14980;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.0 79.1 80.8 82.4 80.8 7 4 6 12 5 28 1.3 N
+0.0400 F11Fcsw_15042;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.6 82.9 79.1 79.9 82.9 21 8 18 5 1 9 1.7 N
+0.0524 F11Fcsw_15664;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 84.6 83.8 71.7 72.9 83.8 41 10 25 3 1 1 0.8 N
+0.0000 F11Fcsw_17394;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0428 F11Fcsw_17898;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 86.7 86.2 71.7 72.5 86.2 45 9 21 2 1 1 0.4 N
+0.0000 F11Fcsw_18564;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_19115;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_19402;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_19500;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0158 F11Fcsw_20028;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N
+0.0161 F11Fcsw_20361;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 77.5 71.4 77.1 73.1 77.1 2 1 3 28 14 33 0.4 N
+0.1919 F11Fcsw_20429;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 84.6 82.1 75.4 73.3 82.1 22 0 5 16 10 22 2.5 N
+0.0158 F11Fcsw_20462;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N
+0.0000 F11Fcsw_20686;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0422 F11Fcsw_21035;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 86.3 84.6 81.3 82.2 84.6 16 4 4 8 4 21 1.7 N
+0.0000 F11Fcsw_21196;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.5878 F11Fcsw_21505;size=1; F11Fcsw_13572;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 92.4 76.7 88.2 72.1 88.2 11 0 0 48 7 13 4.2 Y
+0.0000 F11Fcsw_21636;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_21645;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_21954;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_22687;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_22831;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0322 F11Fcsw_22880;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.3 82.9 70.8 72.5 82.9 41 11 27 2 1 1 0.4 N
+0.0000 F11Fcsw_22900;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_23043;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.5123 F11Fcsw_23322;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 99.2 83.0 97.9 81.7 97.9 3 0 1 40 1 0 1.2 Y
+0.0000 F11Fcsw_23608;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_23684;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0324 F11Fcsw_24087;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.8 83.3 71.2 72.5 83.3 41 11 26 2 1 1 0.4 N
+0.0000 F11Fcsw_24273;size=1; * * * * * * * * 0 0 0 0 0 0 * N
+0.0000 F11Fcsw_24967;size=1; * * * * * * * * 0 0 0 0 0 0 * N
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