# HG changeset patch
# User earlhaminst
# Date 1622030077 0
# Node ID 77cb867e9608881b2caf8f8c9bfa2a296bfade16
# Parent  cf56a65533859aaa0d69a1380a2375a37d6fa15e
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ba755f943aaa8b37434744d32ea0c524503bf50f"

diff -r cf56a6553385 -r 77cb867e9608 lotus2.xml
--- a/lotus2.xml	Wed May 19 19:15:08 2021 +0000
+++ b/lotus2.xml	Wed May 26 11:54:37 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">
+<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.01">
     <description>fast OTU processing pipeline</description>
     <macros>
         <token name="@VERSION@">2.06</token>
@@ -257,7 +257,7 @@
 
     <outputs>
         <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
-        <data name="otu_biom" format="biom" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" />
+        <data name="otu_biom" format="biom1" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" />
         <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
         <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
         <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
diff -r cf56a6553385 -r 77cb867e9608 test-data/hiera_RDP.txt
--- a/test-data/hiera_RDP.txt	Wed May 19 19:15:08 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,188 +0,0 @@
-domain	phylum	class	order	family	genus	species	OTU
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU1
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides	?	OTU2
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Duncaniella	?	OTU3
-Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	?	OTU4
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Phocaeicola	?	OTU5
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	?	?	OTU6
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU7
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU8
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU9
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU10
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Paramuribaculum	?	OTU11
-Bacteria	Campilobacterota	Campylobacteria	Campylobacterales	Helicobacteraceae	Helicobacter	?	OTU12
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU13
-Bacteria	?	?	?	?	?	?	OTU14
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU15
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	?	OTU16
-Bacteria	Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Akkermansiaceae	Akkermansia	?	OTU17
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Acetatifactor	?	OTU18
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU19
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU20
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU21
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Lachnospira	?	OTU22
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU23
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes	?	OTU24
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU25
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU26
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU27
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Muribaculum	?	OTU28
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU29
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Duncaniella	?	OTU30
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU31
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Oscillibacter	?	OTU32
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU33
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU34
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Enterocloster	?	OTU35
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU36
-Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Mailhella	?	OTU37
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU38
-Bacteria	Proteobacteria	Alphaproteobacteria	?	?	?	?	OTU39
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU40
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU41
-Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Limosilactobacillus	?	OTU42
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	?	OTU43
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU44
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU45
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes	?	OTU46
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU47
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Dysosmobacter	?	OTU48
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU49
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Duncaniella	?	OTU50
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU51
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes	?	OTU52
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Butyricicoccus	?	OTU53
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU54
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU55
-Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	?	?	OTU56
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU57
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU58
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU59
-Bacteria	Tenericutes	Mollicutes	Anaeroplasmatales	Anaeroplasmataceae	Anaeroplasma	?	OTU60
-Bacteria	Firmicutes	Clostridia	?	?	?	?	OTU61
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Flintibacter	?	OTU62
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU63
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU64
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	?	OTU65
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU66
-Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Ligilactobacillus	?	OTU67
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU68
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU69
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	?	OTU70
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU71
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	?	?	OTU72
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU73
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU74
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU75
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU76
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Paramuribaculum	?	OTU77
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU78
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU79
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU80
-Bacteria	Firmicutes	Clostridia	Clostridiales	?	?	?	OTU81
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU82
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU83
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Intestinimonas	?	OTU84
-Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	?	?	OTU85
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Clostridium XlVb	?	OTU86
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	?	?	?	OTU87
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU88
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Anaerotignum	?	OTU89
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia	?	OTU90
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU91
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Paramuribaculum	?	OTU92
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU93
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU94
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU95
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Acetatifactor	?	OTU96
-Bacteria	Proteobacteria	Alphaproteobacteria	?	?	?	?	OTU97
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Duncaniella	?	OTU98
-Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Mailhella	?	OTU99
-Bacteria	Firmicutes	Erysipelotrichia	Erysipelotrichales	Erysipelotrichaceae	Amedibacillus	?	OTU100
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Duncaniella	?	OTU101
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU102
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Paramuribaculum	?	OTU103
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Oscillibacter	?	OTU104
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Acutalibacter	?	OTU105
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Duncaniella	?	OTU106
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU107
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU108
-Bacteria	Firmicutes	Clostridia	?	?	?	?	OTU109
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Oscillibacter	?	OTU110
-Bacteria	Deferribacteres	Deferribacteres	Deferribacterales	Deferribacteraceae	Mucispirillum	?	OTU111
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU112
-Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Turicimonas	?	OTU113
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU114
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Phocea	?	OTU115
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Kineothrix	?	OTU116
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU117
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU118
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU119
-Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Mailhella	?	OTU120
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Enterocloster	?	OTU121
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU122
-Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Parasutterella	?	OTU123
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU124
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU125
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU126
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU127
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU128
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU129
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU130
-Bacteria	Firmicutes	Clostridia	Clostridiales	?	?	?	OTU131
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Neglecta	?	OTU132
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU133
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Acetatifactor	?	OTU134
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU135
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU136
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Anaerotruncus	?	OTU137
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU138
-Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Stenotrophomonas	?	OTU139
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU140
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU141
-Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Morganellaceae	Proteus	?	OTU142
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	?	?	?	OTU143
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU144
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU145
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU146
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU147
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU148
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU149
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Acutalibacter	?	OTU150
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU151
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU152
-Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	?	?	OTU153
-Bacteria	Firmicutes	Clostridia	Clostridiales	?	?	?	OTU154
-Bacteria	Firmicutes	Clostridia	Clostridiales	?	?	?	OTU155
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU156
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU157
-Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	?	?	?	OTU158
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU159
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU160
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU161
-Bacteria	Firmicutes	Clostridia	Clostridiales	?	?	?	OTU162
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU163
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU164
-Bacteria	Firmicutes	Clostridia	Clostridiales	?	?	?	OTU165
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU166
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Odoribacteraceae	Odoribacter	?	OTU167
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU168
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU169
-Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Ottowia	?	OTU170
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU171
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Paramuribaculum	?	OTU172
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	Duncaniella	?	OTU173
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides	?	OTU174
-Bacteria	Firmicutes	Clostridia	Clostridiales	?	?	?	OTU175
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae	?	?	OTU176
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU177
-Bacteria	Bacteroidetes	?	?	?	?	?	OTU178
-?	?	?	?	?	?	?	OTU179
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU180
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU181
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU182
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU183
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU184
-Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	?	?	OTU185
-Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	?	?	OTU186
-Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	?	?	OTU187