Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/suite_config.xml @ 7:7bfe1f843858
Support Mothur v1.20
trim.seqs - added name parameter and optional trim.names output
phylo.diversity - group optional, put group and groups in conditional - breaks
get.lineage remove.lineage - allow multiple taxons
dist.shared - added processors
consensus.seqs - add cutoff parameter
trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs
new tools - chimera.uchime deunique.tree count.seqs
shared/relabund files - Column headings
refactor lib/galaxy/datatypes/metagenomics.py
add filters to label and group selects in tool configs
mothur_wrapper.py updated with new tools params
| author | Jim Johnson <jj@umn.edu> |
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| date | Mon, 27 Jun 2011 10:12:25 -0500 |
| parents | e990ac8a0f58 |
| children |
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| 6:ce6e81622c6a | 7:7bfe1f843858 |
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| 1 <suite id="Mothur_toolsuite" name="Mothur Metagenomics" version="1.19.0"> | 1 <suite id="Mothur_toolsuite" name="Mothur Metagenomics" version="1.20.0"> |
| 2 <description>Mothur metagenomics commands as Galaxy tools</description> | 2 <description>Mothur metagenomics commands as Galaxy tools</description> |
| 3 <tool id="mothur_align_check" name="Align.check" version="1.19.0"> | 3 <tool id="mothur_align_check" name="Align.check" version="1.19.0"> |
| 4 <description>Calculate the number of potentially misaligned bases</description> | 4 <description>Calculate the number of potentially misaligned bases</description> |
| 5 </tool> | 5 </tool> |
| 6 <tool id="mothur_align_seqs" name="Align.seqs" version="1.19.0"> | 6 <tool id="mothur_align_seqs" name="Align.seqs" version="1.19.0"> |
| 7 <description>Align sequences to a template alignment</description> | 7 <description>Align sequences to a template alignment</description> |
| 8 </tool> | 8 </tool> |
| 9 <tool id="mothur_amova" name="Amova" version="1.19.0"> | 9 <tool id="mothur_amova" name="Amova" version="1.19.0"> |
| 10 <description>Analysis of molecular variance</description> | 10 <description>Analysis of molecular variance</description> |
| 11 </tool> | 11 </tool> |
| 12 <tool id="mothur_anosim" name="Anosim" version="1.19.0"> | 12 <tool id="mothur_anosim" name="Anosim" version="1.19.0"> |
| 13 <description>Non-parametric multivariate analysis of changes in community structure</description> | 13 <description>Non-parametric multivariate analysis of changes in community structure</description> |
| 14 </tool> | 14 </tool> |
| 15 <tool id="mothur_bin_seqs" name="Bin.seqs" version="1.19.0"> | 15 <tool id="mothur_bin_seqs" name="Bin.seqs" version="1.20.0" force_history_refresh="True"> |
| 16 <description>Order Sequences by OTU</description> | 16 <description>Order Sequences by OTU</description> |
| 17 </tool> | 17 </tool> |
| 18 <tool id="mothur_chimera_bellerophon" name="Chimera.bellerophon" version="1.19.0"> | 18 <tool id="mothur_chimera_bellerophon" name="Chimera.bellerophon" version="1.20.0"> |
| 19 <description>Find putative chimeras using bellerophon</description> | 19 <description>Find putative chimeras using bellerophon</description> |
| 20 </tool> | 20 </tool> |
| 21 <tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.19.0"> | 21 <tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.20.0"> |
| 22 <description>Find putative chimeras using ccode</description> | 22 <description>Find putative chimeras using ccode</description> |
| 23 </tool> | 23 </tool> |
| 24 <tool id="mothur_chimera_check" name="Chimera.check" version="1.19.0"> | 24 <tool id="mothur_chimera_check" name="Chimera.check" version="1.20.0" force_history_refresh="True"> |
| 25 <description>Find putative chimeras using chimeraCheck</description> | 25 <description>Find putative chimeras using chimeraCheck</description> |
| 26 </tool> | 26 </tool> |
| 27 <tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.19.0"> | 27 <tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.20.0"> |
| 28 <description>Find putative chimeras using pintail</description> | 28 <description>Find putative chimeras using pintail</description> |
| 29 </tool> | 29 </tool> |
| 30 <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.19.0"> | 30 <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.20.0"> |
| 31 <description>Find putative chimeras using slayer</description> | 31 <description>Find putative chimeras using slayer</description> |
| 32 </tool> | 32 </tool> |
| 33 <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.19.0"> | 33 <tool id="mothur_chimera_uchime" name="Chimera.uchime" version="1.20.0"> |
| 34 <description>Trim sequences to a specified length</description> | 34 <description>Find putative chimeras using uchime</description> |
| 35 </tool> | 35 </tool> |
| 36 <tool id="mothur_classify_otu" name="Classify.otu" version="1.19.0"> | 36 <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.19.0"> |
| 37 <description>Assign sequences to taxonomy</description> | 37 <description>Trim sequences to a specified length</description> |
| 38 </tool> | 38 </tool> |
| 39 <tool id="mothur_classify_seqs" name="Classify.seqs" version="1.19.0"> | 39 <tool id="mothur_classify_otu" name="Classify.otu" version="1.20.0" force_history_refresh="True"> |
| 40 <description>Assign sequences to taxonomy</description> | 40 <description>Assign sequences to taxonomy</description> |
| 41 </tool> | 41 </tool> |
| 42 <tool id="mothur_clearcut" name="Clearcut" version="1.19.0"> | 42 <tool id="mothur_classify_seqs" name="Classify.seqs" version="1.19.0"> |
| 43 <description>Generate a tree using relaxed neighbor joining</description> | 43 <description>Assign sequences to taxonomy</description> |
| 44 </tool> | 44 </tool> |
| 45 <tool id="mothur_cluster_classic" name="Cluster.classic" version="1.19.0"> | 45 <tool id="mothur_clearcut" name="Clearcut" version="1.19.0"> |
| 46 <description>Assign sequences to OTUs (Dotur implementation)</description> | 46 <description>Generate a tree using relaxed neighbor joining</description> |
| 47 </tool> | 47 </tool> |
| 48 <tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.19.0"> | 48 <tool id="mothur_cluster_classic" name="Cluster.classic" version="1.19.0"> |
| 49 <description> Group sequences that are part of a larger sequence</description> | 49 <description>Assign sequences to OTUs (Dotur implementation)</description> |
| 50 </tool> | 50 </tool> |
| 51 <tool id="mothur_cluster_split" name="Cluster.split" version="1.19.0"> | 51 <tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.20.0"> |
| 52 <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> | 52 <description> Group sequences that are part of a larger sequence</description> |
| 53 </tool> | 53 </tool> |
| 54 <tool id="mothur_cluster" name="Cluster" version="1.19.0"> | 54 <tool id="mothur_cluster_split" name="Cluster.split" version="1.19.0"> |
| 55 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> | 55 <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> |
| 56 </tool> | 56 </tool> |
| 57 <tool id="mothur_collect_shared" name="Collect.shared" version="1.19.0"> | 57 <tool id="mothur_cluster" name="Cluster" version="1.19.0"> |
| 58 <description>Generate collector's curves for calculators on OTUs</description> | 58 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> |
| 59 </tool> | 59 </tool> |
| 60 <tool id="mothur_collect_single" name="Collect.single" version="1.19.0"> | 60 <tool id="mothur_collect_shared" name="Collect.shared" version="1.20.0" force_history_refresh="True"> |
| 61 <description>Generate collector's curves for OTUs</description> | 61 <description>Generate collector's curves for calculators on OTUs</description> |
| 62 </tool> | 62 </tool> |
| 63 <tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.19.0"> | 63 <tool id="mothur_collect_single" name="Collect.single" version="1.20.0" force_history_refresh="True"> |
| 64 <description>Find a consensus sequence for each OTU or phylotype</description> | 64 <description>Generate collector's curves for OTUs</description> |
| 65 </tool> | 65 </tool> |
| 66 <tool id="mothur_corr_axes" name="Corr.axes" version="1.19.0"> | 66 <tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.20.0" force_history_refresh="True"> |
| 67 <description>correlation of data to axes</description> | 67 <description>Find a consensus sequence for each OTU or phylotype</description> |
| 68 </tool> | 68 </tool> |
| 69 <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.19.0"> | 69 <tool id="mothur_corr_axes" name="Corr.axes" version="1.20.0"> |
| 70 <description>Remove gap characters from sequences</description> | 70 <description>correlation of data to axes</description> |
| 71 </tool> | 71 </tool> |
| 72 <tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.19.0"> | 72 <tool id="mothur_count_seqs" name="Count.seqs" version="1.20.0" > |
| 73 <description>Return all sequences</description> | 73 <description>counts the number of sequences represented by the representative</description> |
| 74 </tool> | 74 </tool> |
| 75 <tool id="mothur_dist_seqs" name="Dist.seqs" version="1.19.0"> | 75 <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.20.0"> |
| 76 <description>calculate uncorrected pairwise distances between aligned sequences</description> | 76 <description>Remove gap characters from sequences</description> |
| 77 </tool> | 77 </tool> |
| 78 <tool id="mothur_dist_shared" name="Dist.shared" version="1.19.0"> | 78 <tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.20.0"> |
| 79 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> | 79 <description>Return all sequences</description> |
| 80 </tool> | 80 </tool> |
| 81 <tool id="mothur_fastq_info" name="Fastq.info" version="1.19.0"> | 81 <tool id="mothur_deunique_tree" name="Deunique.tree" version="1.20.0"> |
| 82 <description>Convert fastq to fasta and quality</description> | 82 <description>Reinsert the redundant sequence identiers back into a unique tree.</description> |
| 83 </tool> | 83 </tool> |
| 84 <tool id="mothur_filter_seqs" name="Filter.seqs" version="1.19.0"> | 84 <tool id="mothur_dist_seqs" name="Dist.seqs" version="1.19.0"> |
| 85 <description>removes columns from alignments</description> | 85 <description>calculate uncorrected pairwise distances between aligned sequences</description> |
| 86 </tool> | 86 </tool> |
| 87 <tool id="mothur_get_groups" name="Get.groups" version="1.19.0"> | 87 <tool id="mothur_dist_shared" name="Dist.shared" version="1.20.0" force_history_refresh="True"> |
| 88 <description>Select groups</description> | 88 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> |
| 89 </tool> | 89 </tool> |
| 90 <tool id="mothur_get_group" name="Get.group" version="1.19.0"> | 90 <tool id="mothur_fastq_info" name="Fastq.info" version="1.19.0"> |
| 91 <description>group names from shared or from list and group</description> | 91 <description>Convert fastq to fasta and quality</description> |
| 92 </tool> | 92 </tool> |
| 93 <tool id="mothur_get_lineage" name="Get.lineage" version="1.19.0"> | 93 <tool id="mothur_filter_seqs" name="Filter.seqs" version="1.19.0" force_history_refresh="True"> |
| 94 <description>Picks by taxon</description> | 94 <description>removes columns from alignments</description> |
| 95 </tool> | 95 </tool> |
| 96 <tool id="mothur_get_otulist" name="Get.otulist" version="1.19.0"> | 96 <tool id="mothur_get_groups" name="Get.groups" version="1.20.0"> |
| 97 <description>Get otus for each distance in a otu list</description> | 97 <description>Select groups</description> |
| 98 </tool> | 98 </tool> |
| 99 <tool id="mothur_get_oturep" name="Get.oturep" version="1.19.0"> | 99 <tool id="mothur_get_group" name="Get.group" version="1.19.0"> |
| 100 <description>Generate a fasta with a representative sequence for each OTU</description> | 100 <description>group names from shared or from list and group</description> |
| 101 </tool> | 101 </tool> |
| 102 <tool id="mothur_get_otus" name="Get.otus" version="1.19.0"> | 102 <tool id="mothur_get_lineage" name="Get.lineage" version="1.20.0"> |
| 103 <description>Get otus containing sequences from specified groups</description> | 103 <description>Picks by taxon</description> |
| 104 </tool> | 104 </tool> |
| 105 <tool id="mothur_get_rabund" name="Get.rabund" version="1.19.0"> | 105 <tool id="mothur_get_otulist" name="Get.otulist" force_history_refresh="True" version="1.19.0"> |
| 106 <description>Get rabund from a otu list or sabund</description> | 106 <description>Get otus for each distance in a otu list</description> |
| 107 </tool> | 107 </tool> |
| 108 <tool id="mothur_get_relabund" name="Get.relabund" version="1.19.0"> | 108 <tool id="mothur_get_oturep" name="Get.oturep" version="1.20.0" force_history_refresh="True"> |
| 109 <description>Calculate the relative abundance of each otu</description> | 109 <description>Generate a fasta with a representative sequence for each OTU</description> |
| 110 </tool> | 110 </tool> |
| 111 <tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0"> | 111 <tool id="mothur_get_otus" name="Get.otus" version="1.19.0"> |
| 112 <description>Get sabund from a otu list or rabund</description> | 112 <description>Get otus containing sequences from specified groups</description> |
| 113 </tool> | 113 </tool> |
| 114 <tool id="mothur_get_seqs" name="Get.seqs" version="1.19.0"> | 114 <tool id="mothur_get_rabund" name="Get.rabund" version="1.19.0"> |
| 115 <description>Picks sequences by name</description> | 115 <description>Get rabund from a otu list or sabund</description> |
| 116 </tool> | 116 </tool> |
| 117 <tool id="mothur_get_sharedseqs" name="Get.sharedseqs" version="1.19.0"> | 117 <tool id="mothur_get_relabund" name="Get.relabund" version="1.20.0"> |
| 118 <description>Get shared sequences at each distance from list and group</description> | 118 <description>Calculate the relative abundance of each otu</description> |
| 119 </tool> | 119 </tool> |
| 120 <tool id="mothur_hcluster" name="Hcluster" version="1.19.0"> | 120 <tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0"> |
| 121 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> | 121 <description>Get sabund from a otu list or rabund</description> |
| 122 </tool> | 122 </tool> |
| 123 <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.19.0"> | 123 <tool id="mothur_get_seqs" name="Get.seqs" version="1.20.0"> |
| 124 <description>Generate a heatmap for OTUs</description> | 124 <description>Picks sequences by name</description> |
| 125 </tool> | 125 </tool> |
| 126 <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.19.0"> | 126 <tool id="mothur_get_sharedseqs" name="Get.sharedseqs" version="1.20.0" force_history_refresh="True"> |
| 127 <description>Generate a heatmap for pariwise similarity</description> | 127 <description>Get shared sequences at each distance from list and group</description> |
| 128 </tool> | 128 </tool> |
| 129 <tool id="mothur_homova" name="Homova" version="1.19.0"> | 129 <tool id="mothur_hcluster" name="Hcluster" version="1.19.0"> |
| 130 <description>Homogeneity of molecular variance</description> | 130 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> |
| 131 </tool> | 131 </tool> |
| 132 <tool id="mothur_indicator" name="Indicator" version="1.19.0"> | 132 <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.20.0" force_history_refresh="True"> |
| 133 <description>Identify indicator "species" for nodes on a tree</description> | 133 <description>Generate a heatmap for OTUs</description> |
| 134 </tool> | 134 </tool> |
| 135 <tool id="mothur_libshuff" name="Libshuff" version="1.19.0"> | 135 <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.20.0" force_history_refresh="True"> |
| 136 <description>Cramer-von Mises tests communities for the same structure</description> | 136 <description>Generate a heatmap for pariwise similarity</description> |
| 137 </tool> | 137 </tool> |
| 138 <tool id="mothur_list_seqs" name="List.seqs" version="1.19.0"> | 138 <tool id="mothur_homova" name="Homova" version="1.19.0"> |
| 139 <description>Lists the names (accnos) of the sequences</description> | 139 <description>Homogeneity of molecular variance</description> |
| 140 </tool> | 140 </tool> |
| 141 <tool id="mothur_make_design" name="Make Design" version="1.19.0" > | 141 <tool id="mothur_indicator" name="Indicator" version="1.20.0"> |
| 142 <description>Assign groups to Sets</description> | 142 <description>Identify indicator "species" for nodes on a tree</description> |
| 143 </tool> | 143 </tool> |
| 144 <tool id="mothur_make_fastq" name="Make.fastq" version="1.19.0"> | 144 <tool id="mothur_libshuff" name="Libshuff" version="1.19.0"> |
| 145 <description>Convert fasta and quality to fastq</description> | 145 <description>Cramer-von Mises tests communities for the same structure</description> |
| 146 </tool> | 146 </tool> |
| 147 <tool id="mothur_make_files" name="Make.group" version="1.19.0"> | 147 <tool id="mothur_list_seqs" name="List.seqs" version="1.19.0"> |
| 148 <description>Make a group file</description> | 148 <description>Lists the names (accnos) of the sequences</description> |
| 149 </tool> | 149 </tool> |
| 150 <tool id="mothur_make_shared" name="Make.shared" version="1.19.0"> | 150 <tool id="mothur_make_design" name="Make Design" version="1.19.0" > |
| 151 <description>Make a shared file from a list and a group</description> | 151 <description>Assign groups to Sets</description> |
| 152 </tool> | 152 </tool> |
| 153 <tool id="mothur_mantel" name="Mantel" version="1.19.0"> | 153 <tool id="mothur_make_fastq" name="Make.fastq" version="1.19.0"> |
| 154 <description>Mantel correlation coefficient between two matrices.</description> | 154 <description>Convert fasta and quality to fastq</description> |
| 155 </tool> | 155 </tool> |
| 156 <tool id="mothur_merge_files" name="Merge.files" version="1.19.0"> | 156 <tool id="mothur_make_files" name="Make.group" version="1.19.0"> |
| 157 <description>Merge data</description> | 157 <description>Make a group file</description> |
| 158 </tool> | 158 </tool> |
| 159 <tool id="mothur_merge_groups" name="Merge.groups" version="1.19.0" > | 159 <tool id="mothur_make_shared" name="Make.shared" version="1.19.0" force_history_refresh="True"> |
| 160 <description>Merge groups in a shared file</description> | 160 <description>Make a shared file from a list and a group</description> |
| 161 </tool> | 161 </tool> |
| 162 <tool id="mothur_metastats" name="Metastats" version="1.19.0" > | 162 <tool id="mothur_mantel" name="Mantel" version="1.19.0"> |
| 163 <description>generate principle components plot data</description> | 163 <description>Mantel correlation coefficient between two matrices.</description> |
| 164 </tool> | 164 </tool> |
| 165 <tool id="mothur_nmds" name="Nmds" version="1.19.0"> | 165 <tool id="mothur_merge_files" name="Merge.files" version="1.19.0"> |
| 166 <description>generate non-metric multidimensional scaling data</description> | 166 <description>Merge data</description> |
| 167 </tool> | 167 </tool> |
| 168 <tool id="mothur_normalize_shared" name="Normalize.shared" version="1.19.0"> | 168 <tool id="mothur_merge_groups" name="Merge.groups" version="1.20.0" > |
| 169 <description>Normalize the number of sequences per group to a specified level</description> | 169 <description>Merge groups in a shared file</description> |
| 170 </tool> | 170 </tool> |
| 171 <tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.19.0"> | 171 <tool id="mothur_metastats" name="Metastats" version="1.20.0" force_history_refresh="True" > |
| 172 <description>Relate OTUs at different distances</description> | 172 <description>generate principle components plot data</description> |
| 173 </tool> | 173 </tool> |
| 174 <tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.19.0"> | 174 <tool id="mothur_nmds" name="Nmds" version="1.19.0"> |
| 175 <description>calculate uncorrected pairwise distances between sequences</description> | 175 <description>generate non-metric multidimensional scaling data</description> |
| 176 </tool> | 176 </tool> |
| 177 <tool id="mothur_parse_list" name="Parse.list" version="1.19.0"> | 177 <tool id="mothur_normalize_shared" name="Normalize.shared" version="1.20.0"> |
| 178 <description>Generate a List file for each group</description> | 178 <description>Normalize the number of sequences per group to a specified level</description> |
| 179 </tool> | 179 </tool> |
| 180 <tool id="mothur_parsimony" name="Parsimony" version="1.19.0"> | 180 <tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.19.0"> |
| 181 <description>Describes whether two or more communities have the same structure</description> | 181 <description>Relate OTUs at different distances</description> |
| 182 </tool> | 182 </tool> |
| 183 <tool id="mothur_pca" name="Pca" version="1.19.0"> | 183 <tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.19.0"> |
| 184 <description>Principal Coordinate Analysis for a shared file</description> | 184 <description>calculate uncorrected pairwise distances between sequences</description> |
| 185 </tool> | 185 </tool> |
| 186 <tool id="mothur_pcoa" name="Pcoa" version="1.19.0" > | 186 <tool id="mothur_parse_list" name="Parse.list" version="1.19.0" force_history_refresh="True"> |
| 187 <description>Principal Coordinate Analysis for a distance matrix</description> | 187 <description>Generate a List file for each group</description> |
| 188 </tool> | 188 </tool> |
| 189 <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.19.0"> | 189 <tool id="mothur_parsimony" name="Parsimony" version="1.19.0"> |
| 190 <description>Alpha Diversity calculates unique branch length</description> | 190 <description>Describes whether two or more communities have the same structure</description> |
| 191 </tool> | 191 </tool> |
| 192 <tool id="mothur_phylotype" name="Phylotype" version="1.19.0"> | 192 <tool id="mothur_pca" name="Pca" version="1.20.0"> |
| 193 <description>Assign sequences to OTUs based on taxonomy</description> | 193 <description>Principal Coordinate Analysis for a shared file</description> |
| 194 </tool> | 194 </tool> |
| 195 <tool id="mothur_pre_cluster" name="Pre.cluster" version="1.19.0"> | 195 <tool id="mothur_pcoa" name="Pcoa" version="1.19.0" > |
| 196 <description>Remove sequences due to pyrosequencing errors</description> | 196 <description>Principal Coordinate Analysis for a distance matrix</description> |
| 197 </tool> | 197 </tool> |
| 198 <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.19.0"> | 198 <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.20.0"> |
| 199 <description>Generate inter-sample rarefaction curves for OTUs</description> | 199 <description>Alpha Diversity calculates unique branch length</description> |
| 200 </tool> | 200 </tool> |
| 201 <tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.19.0"> | 201 <tool id="mothur_phylotype" name="Phylotype" version="1.19.0"> |
| 202 <description>Generate intra-sample rarefaction curves for OTUs</description> | 202 <description>Assign sequences to OTUs based on taxonomy</description> |
| 203 </tool> | 203 </tool> |
| 204 <tool id="mothur_remove_groups" name="Remove.groups" version="1.19.0"> | 204 <tool id="mothur_pre_cluster" name="Pre.cluster" version="1.20.0"> |
| 205 <description>Remove groups from groups,fasta,names,list,taxonomy</description> | 205 <description>Remove sequences due to pyrosequencing errors</description> |
| 206 </tool> | 206 </tool> |
| 207 <tool id="mothur_remove_lineage" name="Remove.lineage" version="1.19.0"> | 207 <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.20.0"> |
| 208 <description>Picks by taxon</description> | 208 <description>Generate inter-sample rarefaction curves for OTUs</description> |
| 209 </tool> | 209 </tool> |
| 210 <tool id="mothur_remove_otus" name="Remove.otus" version="1.19.0"> | 210 <tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.20.0" force_history_refresh="True"> |
| 211 <description>Remove otus containing sequences from specified groups</description> | 211 <description>Generate intra-sample rarefaction curves for OTUs</description> |
| 212 </tool> | 212 </tool> |
| 213 <tool id="mothur_remove_rare" name="Remove.rare" version="1.19.0"> | 213 <tool id="mothur_remove_groups" name="Remove.groups" version="1.19.0"> |
| 214 <description>Remove rare OTUs</description> | 214 <description>Remove groups from groups,fasta,names,list,taxonomy</description> |
| 215 </tool> | 215 </tool> |
| 216 <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.19.0"> | 216 <tool id="mothur_remove_lineage" name="Remove.lineage" version="1.20.0"> |
| 217 <description>Remove sequences by name</description> | 217 <description>Picks by taxon</description> |
| 218 </tool> | 218 </tool> |
| 219 <tool id="mothur_reverse_seqs" name="Reverse.seqs" version="1.19.0"> | 219 <tool id="mothur_remove_otus" name="Remove.otus" version="1.19.0"> |
| 220 <description>Reverse complement the sequences</description> | 220 <description>Remove otus containing sequences from specified groups</description> |
| 221 </tool> | 221 </tool> |
| 222 <tool id="mothur_screen_seqs" name="Screen.seqs" version="1.19.0"> | 222 <tool id="mothur_remove_rare" name="Remove.rare" version="1.20.0"> |
| 223 <description>Screen sequences</description> | 223 <description>Remove rare OTUs</description> |
| 224 </tool> | 224 </tool> |
| 225 <tool id="mothur_sens_spec" name="Sens.spec" version="1.19.0" > | 225 <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.20.0"> |
| 226 <description>Determine the quality of OTU assignment</description> | 226 <description>Remove sequences by name</description> |
| 227 </tool> | 227 </tool> |
| 228 <tool id="mothur_sffinfo" name="Sffinfo" version="1.19.0"> | 228 <tool id="mothur_reverse_seqs" name="Reverse.seqs" version="1.19.0"> |
| 229 <description>Summarize the quality of sequences</description> | 229 <description>Reverse complement the sequences</description> |
| 230 </tool> | 230 </tool> |
| 231 <tool id="mothur_split_abund" name="Split.abund" version="1.19.0"> | 231 <tool id="mothur_screen_seqs" name="Screen.seqs" version="1.20.0"> |
| 232 <description>Separate sequences into rare and abundant groups</description> | 232 <description>Screen sequences</description> |
| 233 </tool> | 233 </tool> |
| 234 <tool id="mothur_split_groups" name="Split.groups" version="1.19.0"> | 234 <tool id="mothur_sens_spec" name="Sens.spec" version="1.19.0" > |
| 235 <description>Generates a fasta file for each group</description> | 235 <description>Determine the quality of OTU assignment</description> |
| 236 </tool> | 236 </tool> |
| 237 <tool id="mothur_sub_sample" name="Sub.sample" version="1.19.0"> | 237 <tool id="mothur_sffinfo" name="Sffinfo" version="1.19.0"> |
| 238 <description>Create a sub sample</description> | 238 <description>Summarize the quality of sequences</description> |
| 239 </tool> | 239 </tool> |
| 240 <tool id="mothur_summary_seqs" name="Summary.seqs" version="1.19.0"> | 240 <tool id="mothur_split_abund" name="Split.abund" version="1.20.0" force_history_refresh="True"> |
| 241 <description>Summarize the quality of sequences</description> | 241 <description>Separate sequences into rare and abundant groups</description> |
| 242 </tool> | 242 </tool> |
| 243 <tool id="mothur_summary_shared" name="Summary.shared" version="1.19.0"> | 243 <tool id="mothur_split_groups" name="Split.groups" version="1.20.0" force_history_refresh="True"> |
| 244 <description>Summary of calculator values for OTUs</description> | 244 <description>Generates a fasta file for each group</description> |
| 245 </tool> | 245 </tool> |
| 246 <tool id="mothur_summary_single" name="Summary.single" version="1.19.0"> | 246 <tool id="mothur_sub_sample" name="Sub.sample" version="1.20.0"> |
| 247 <description>Summary of calculator values for OTUs</description> | 247 <description>Create a sub sample</description> |
| 248 </tool> | 248 </tool> |
| 249 <tool id="mothur_tree_shared" name="Tree.shared" version="1.19.0"> | 249 <tool id="mothur_summary_seqs" name="Summary.seqs" version="1.19.0"> |
| 250 <description>Generate a newick tree for dissimilarity among groups</description> | 250 <description>Summarize the quality of sequences</description> |
| 251 </tool> | 251 </tool> |
| 252 <tool id="tree_vector" name="TreeVector" version="1.0"> | 252 <tool id="mothur_summary_shared" name="Summary.shared" version="1.20.0" force_history_refresh="True"> |
| 253 <description>Draw a Phylogenic Tree</description> | 253 <description>Summary of calculator values for OTUs</description> |
| 254 </tool> | 254 </tool> |
| 255 <tool id="mothur_trim_seqs" name="Trim.seqs" version="1.19.0"> | 255 <tool id="mothur_summary_single" name="Summary.single" version="1.19.0" force_history_refresh="True"> |
| 256 <description>Trim sequences - primers, barcodes, quality</description> | 256 <description>Summary of calculator values for OTUs</description> |
| 257 </tool> | 257 </tool> |
| 258 <tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.19.0"> | 258 <tool id="mothur_tree_shared" name="Tree.shared" version="1.20.0" force_history_refresh="True"> |
| 259 <description>Describes whether two or more communities have the same structure</description> | 259 <description>Generate a newick tree for dissimilarity among groups</description> |
| 260 </tool> | 260 </tool> |
| 261 <tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.19.0"> | 261 <tool id="tree_vector" name="TreeVector" version="1.0"> |
| 262 <description>Describes whether two or more communities have the same structure</description> | 262 <description>Draw a Phylogenic Tree</description> |
| 263 </tool> | 263 </tool> |
| 264 <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.19.0"> | 264 <tool id="mothur_trim_seqs" name="Trim.seqs" version="1.20.0" force_history_refresh="True"> |
| 265 <description>Return unique sequences</description> | 265 <description>Trim sequences - primers, barcodes, quality</description> |
| 266 </tool> | 266 </tool> |
| 267 <tool id="mothur_venn" name="Venn" version="1.19.0"> | 267 <tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.19.0"> |
| 268 <description>Generate Venn diagrams for groups </description> | 268 <description>Describes whether two or more communities have the same structure</description> |
| 269 </tool> | 269 </tool> |
| 270 <tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.19.0"> | |
| 271 <description>Describes whether two or more communities have the same structure</description> | |
| 272 </tool> | |
| 273 <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.20.0"> | |
| 274 <description>Return unique sequences</description> | |
| 275 </tool> | |
| 276 <tool id="mothur_venn" name="Venn" version="1.20.0" force_history_refresh="True"> | |
| 277 <description>Generate Venn diagrams for groups </description> | |
| 278 </tool> | |
| 270 </suite> | 279 </suite> |