diff mothur/suite_config.xml @ 1:c7923b34dea4

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- a/mothur/suite_config.xml	Tue Jun 07 16:54:12 2011 -0400
+++ b/mothur/suite_config.xml	Tue Jun 07 17:01:07 2011 -0400
@@ -1,210 +1,240 @@
-<suite id="Mothur_toolsuite" name="Mothur Metagenomics" version="1.15.1">
+<suite id="Mothur_toolsuite" name="Mothur Metagenomics" version="1.16.0">
   <description>Mothur metagenomics commands as Galaxy tools</description>
-    <tool id="mothur_align_check" name="Align.check" version="1.15.0">
+    <tool id="mothur_align_check" name="Align.check" version="1.16.0">
      <description>Calculate the number of potentially misaligned bases</description>
     </tool>
-    <tool id="mothur_align_seqs" name="Align.seqs" version="1.15.0">
+    <tool id="mothur_align_seqs" name="Align.seqs" version="1.16.0">
      <description>Align sequences to a template alignment</description>
     </tool>
-    <tool id="mothur_bin_seqs" name="Bin.seqs" version="1.15.0">
+    <tool id="mothur_bin_seqs" name="Bin.seqs" version="1.16.0" force_history_refresh="True">
      <description>Order Sequences by OTU</description>
     </tool>
-    <tool id="mothur_chimera_bellerophon" name="Chimera.bellerophon" version="1.15.0">
+    <tool id="mothur_bootstrap_shared" name="Bootstrap.shared" version="1.16.0" force_history_refresh="True">
+     <description>Generate a newick trees for dissimilarity among groups</description>
+    </tool>
+    <tool id="mothur_chimera_bellerophon" name="Chimera.bellerophon" version="1.16.0">
      <description>Find putative chimeras using bellerophon</description>
     </tool>
-    <tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.15.0">
+    <tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.16.0">
      <description>Find putative chimeras using ccode</description>
     </tool>
-    <tool id="mothur_chimera_check" name="Chimera.check" version="1.15.0">
+    <tool id="mothur_chimera_check" name="Chimera.check" version="1.16.0" force_history_refresh="True">
      <description>Find putative chimeras using chimeraCheck</description>
     </tool>
-    <tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.15.0">
+    <tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.16.0">
      <description>Find putative chimeras using pintail</description>
     </tool>
-    <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.15.0">
+    <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.16.0">
      <description>Find putative chimeras using slayer</description>
     </tool>
-    <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.15.0">
+    <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.16.0">
      <description>Trim sequences to a specified length</description>
     </tool>
-    <tool id="mothur_classify_otu" name="Classify.otu" version="1.15.0">
+    <tool id="mothur_classify_otu" name="Classify.otu" version="1.16.0" force_history_refresh="True">
      <description>Assign sequences to taxonomy</description>
     </tool>
-    <tool id="mothur_classify_seqs" name="Classify.seqs" version="1.15.0">
+    <tool id="mothur_classify_seqs" name="Classify.seqs" version="1.16.0">
      <description>Assign sequences to taxonomy</description>
     </tool>
-    <tool id="mothur_clearcut" name="Clearcut" version="1.15.0">
+    <tool id="mothur_clearcut" name="Clearcut" version="1.16.0">
      <description>Generate a tree using relaxed neighbor joining</description>
     </tool>
-    <tool id="mothur_cluster_classic" name="Cluster.classic" version="1.15.0">
+    <tool id="mothur_cluster_classic" name="Cluster.classic" version="1.16.0">
      <description>Assign sequences to OTUs (Dotur implementation)</description>
     </tool>
-    <tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.15.0">
+    <tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.16.0">
      <description> Group sequences that are part of a larger sequence</description>
     </tool>
-    <tool id="mothur_cluster" name="Cluster" version="1.15.0">
+    <tool id="mothur_cluster_split" name="Cluster.split" version="1.16.0">
+     <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description>
+    </tool>
+    <tool id="mothur_cluster" name="Cluster" version="1.16.0">
      <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
     </tool>
-    <tool id="mothur_collect_shared" name="Collect.shared" version="1.15.0">
+    <tool id="mothur_collect_shared" name="Collect.shared" version="1.16.0" force_history_refresh="True">
      <description>Generate collector's curves for calculators on OTUs</description>
     </tool>
-    <tool id="mothur_collect_single" name="Collect.single" version="1.15.0">
+    <tool id="mothur_collect_single" name="Collect.single" version="1.16.0" force_history_refresh="True">
      <description>Summary of calculator values for OTUs</description>
     </tool>
-    <tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.15.0">
+    <tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.16.0" force_history_refresh="True">
      <description>Find a consensus sequence for each OTU or phylotype</description>
     </tool>
-    <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.15.0">
+    <tool id="mothur_corr_axes" name="Corr.axes" version="1.16.0">
+     <description>correlation of data to axes</description>
+    </tool>
+    <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.16.0">
      <description>Remove gap characters from sequences</description>
     </tool>
-    <tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.15.0">
+    <tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.16.0">
      <description>Return all sequences</description>
     </tool>
-    <tool id="mothur_dist_seqs" name="Dist.seqs" version="1.15.0">
+    <tool id="mothur_dist_seqs" name="Dist.seqs" version="1.16.0">
      <description>calculate uncorrected pairwise distances between aligned sequences</description>
     </tool>
-    <tool id="mothur_dist_shared" name="Dist.shared" version="1.15.0">
+    <tool id="mothur_dist_shared" name="Dist.shared" version="1.16.0" force_history_refresh="True">
      <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
     </tool>
-    <tool id="mothur_fastq_info" name="Fastq.info" version="1.15.0">
+    <tool id="mothur_fastq_info" name="Fastq.info" version="1.16.0">
      <description>Convert fastq to fasta and quality</description>
     </tool>
-    <tool id="mothur_filter_seqs" name="Filter.seqs" version="1.15.0">
+    <tool id="mothur_filter_seqs" name="Filter.seqs" version="1.16.0" force_history_refresh="True">
      <description>removes columns from alignments</description>
     </tool>
-    <tool id="mothur_get_groups" name="Get.groups" version="1.15.0">
+    <tool id="mothur_get_groups" name="Get.groups" version="1.16.0">
      <description>Select groups</description>
     </tool>
-    <tool id="mothur_get_lineage" name="Get.lineage" version="1.15.0">
+    <tool id="mothur_get_group" name="Get.group" version="1.16.0">
+     <description>group names from shared or from list and group</description>
+    </tool>
+    <tool id="mothur_get_lineage" name="Get.lineage" version="1.16.0">
      <description>Picks by taxon</description>
     </tool>
-    <tool id="mothur_get_oturep" name="Get.oturep" version="1.15.0" >
+    <tool id="mothur_get_oturep" name="Get.oturep" version="1.16.0"  force_history_refresh="True">
      <description>Generate a fasta with a representative sequence for each OTU</description>
     </tool>
-    <tool id="mothur_get_otus" name="Get.otus" version="1.15.0">
+    <tool id="mothur_get_otus" name="Get.otus" version="1.16.0">
      <description>Get otus containing sequences from specified groups</description>
     </tool>
-    <tool id="mothur_get_relabund" name="Get.relabund" version="1.15.0">
+    <tool id="mothur_get_relabund" name="Get.relabund" version="1.16.0">
      <description>Calculate the relative abundance of each otu</description>
     </tool>
-    <tool id="mothur_get_seqs" name="Get.seqs" version="1.15.0">
+    <tool id="mothur_get_seqs" name="Get.seqs" version="1.16.0">
      <description>Picks sequences by name</description>
     </tool>
-    <tool id="mothur_hcluster" name="Hcluster" version="1.15.0">
+    <tool id="mothur_hcluster" name="Hcluster" version="1.16.0">
      <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
     </tool>
-    <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.15.0" >
+    <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.16.0"  force_history_refresh="True">
      <description>Generate a heatmap for OTUs</description>
     </tool>
-    <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.15.0" >
+    <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.16.0"  force_history_refresh="True">
      <description>Generate a heatmap for pariwise similarity</description>
     </tool>
-    <tool id="mothur_indicator" name="Indicator" version="1.15.0">
+    <tool id="mothur_indicator" name="Indicator" version="1.16.0">
      <description>Identify indicator "species" for nodes on a tree</description>
     </tool>
-    <tool id="mothur_libshuff" name="Libshuff" version="1.15.0">
+    <tool id="mothur_libshuff" name="Libshuff" version="1.16.0">
      <description>Cramer-von Mises tests communities for the same structure</description>
     </tool>
-    <tool id="mothur_list_seqs" name="List.seqs" version="1.15.0">
+    <tool id="mothur_list_seqs" name="List.seqs" version="1.16.0">
      <description>Lists the names of the sequences</description>
     </tool>
-    <tool id="mothur_make_files" name="Make.group" version="1.15.0">
+    <tool id="mothur_make_design" name="Make Design" version="1.16.0" >
+     <description>Assign groups to Sets</description>
+    </tool>
+    <tool id="mothur_make_files" name="Make.group" version="1.16.0">
      <description>Make a group file</description>
     </tool>
-    <tool id="mothur_merge_files" name="Merge.files" version="1.15.0">
+    <tool id="mothur_merge_files" name="Merge.files" version="1.16.0">
      <description>Merge data</description>
     </tool>
-    <tool id="mothur_normalize_shared" name="Normalize.shared" version="1.15.0">
+    <tool id="mothur_merge_groups" name="Merge.groups" version="1.16.0" >
+     <description>Merge groups in a shared file</description>
+    </tool>
+    <tool id="mothur_metastats" name="Metastats" version="1.16.0">
+     <description>generate principle components plot data</description>
+    </tool>
+    <tool id="mothur_nmds" name="Nmds" version="1.16.0">
+     <description>generate non-metric multidimensional scaling data</description>
+    </tool>
+    <tool id="mothur_normalize_shared" name="Normalize.shared" version="1.16.0">
      <description>Normalize the number of sequences per group to a specified level</description>
     </tool>
-    <tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.15.0">
+    <tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.16.0">
      <description>calculate uncorrected pairwise distances between sequences</description>
     </tool>
-    <tool id="mothur_parse_list" name="Parse.list" version="1.15.0">
+    <tool id="mothur_parse_list" name="Parse.list" version="1.16.0" force_history_refresh="True">
      <description>Order Sequences by OTU</description>
     </tool>
-    <tool id="mothur_parsimony" name="Parsimony" version="1.15.0">
+    <tool id="mothur_parsimony" name="Parsimony" version="1.16.0">
      <description>Describes whether two or more communities have the same structure</description>
     </tool>
-    <tool id="mothur_pcoa" name="Pcoa" version="1.15.0" >
+    <tool id="mothur_pca" name="Pca" version="1.16.0">
+     <description>generate principle components plot data</description>
+    </tool>
+    <tool id="mothur_pcoa" name="Pcoa" version="1.16.0" >
      <description>Principal Coordinate Analysis</description>
     </tool>
-    <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.15.0">
+    <tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.16.0">
      <description>Alpha Diversity calculate unique branch length</description>
     </tool>
-    <tool id="mothur_phylotype" name="Phylotype" version="1.15.0">
+    <tool id="mothur_phylotype" name="Phylotype" version="1.16.0">
      <description>Assign sequences to OTUs based on taxonomy</description>
     </tool>
-    <tool id="mothur_pre_cluster" name="Pre.cluster" version="1.15.0">
+    <tool id="mothur_pre_cluster" name="Pre.cluster" version="1.16.0">
      <description>Remove sequences due to pyrosequencing errors</description>
     </tool>
-    <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.15.0">
+    <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.16.0">
      <description>Generate inter-sample rarefaction curves for OTUs</description>
     </tool>
-    <tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.15.0">
+    <tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.16.0" force_history_refresh="True">
      <description>Generate intra-sample rarefaction curves for OTUs</description>
     </tool>
-    <tool id="mothur_read_otu" name="Read.otu" version="1.15.0">
+    <tool id="mothur_read_otu" name="Read.otu" version="1.16.0" force_history_refresh="True">
      <description>Read OTU list and group to create a shared file</description>
     </tool>
-    <tool id="mothur_remove_groups" name="Remove.groups" version="1.15.0">
+    <tool id="mothur_remove_groups" name="Remove.groups" version="1.16.0">
      <description>Remove groups</description>
     </tool>
-    <tool id="mothur_remove_lineage" name="Remove.lineage" version="1.15.0">
+    <tool id="mothur_remove_lineage" name="Remove.lineage" version="1.16.0">
      <description>Picks by taxon</description>
     </tool>
-    <tool id="mothur_remove_otus" name="Remove.otus" version="1.15.0">
+    <tool id="mothur_remove_otus" name="Remove.otus" version="1.16.0">
      <description>Remove otus containing sequences from specified groups</description>
     </tool>
-    <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.15.0">
+    <tool id="mothur_remove_rare" name="Remove.rare" version="1.16.0">
+     <description>Remove rare OTUs</description>
+    </tool>
+    <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.16.0">
      <description>Remove sequences by name</description>
     </tool>
-    <tool id="mothur_reverse_seqs" name="Reverse.seqs" version="1.15.0">
+    <tool id="mothur_reverse_seqs" name="Reverse.seqs" version="1.16.0">
      <description>Reverse complement the sequences</description>
     </tool>
-    <tool id="mothur_screen_seqs" name="Screen.seqs" version="1.15.0">
+    <tool id="mothur_screen_seqs" name="Screen.seqs" version="1.16.0">
      <description>Screen sequences</description>
     </tool>
-    <tool id="mothur_sffinfo" name="Sffinfo" version="1.15.0">
+    <tool id="mothur_sffinfo" name="Sffinfo" version="1.16.0">
      <description>Summarize the quality of sequences</description>
     </tool>
-    <tool id="mothur_split_abund" name="Split.abund" version="1.15.0">
+    <tool id="mothur_split_abund" name="Split.abund" version="1.16.0" force_history_refresh="True">
      <description>Separate sequences into rare and abundant groups</description>
     </tool>
-    <tool id="mothur_split_groups" name="Split.groups" version="1.15.0">
+    <tool id="mothur_split_groups" name="Split.groups" version="1.16.0" force_history_refresh="True">
      <description>Generates a fasta file for each group</description>
     </tool>
-    <tool id="mothur_sub_sample" name="Sub.sample" version="1.15.0">
+    <tool id="mothur_sub_sample" name="Sub.sample" version="1.16.0">
      <description>Create a sub sample</description>
     </tool>
-    <tool id="mothur_summary_seqs" name="Summary.seqs" version="1.15.0">
+    <tool id="mothur_summary_seqs" name="Summary.seqs" version="1.16.0">
      <description>Summarize the quality of sequences</description>
     </tool>
-    <tool id="mothur_summary_shared" name="Summary.shared" version="1.15.0" >
-     <description>Summary of calculator values for OTUs</description>
-    </tool>
-    <tool id="mothur_summary_single" name="Summary.single" version="1.15.0">
+    <tool id="mothur_summary_shared" name="Summary.shared" version="1.16.0"  force_history_refresh="True">
      <description>Summary of calculator values for OTUs</description>
     </tool>
-    <tool id="mothur_tree_shared" name="Tree.shared" version="1.15.0">
-     <description>Generate a newick tree for dissimilarity among groups</description>
-    </tool>
-    <tool id="mothur_trim_seqs" name="Trim.seqs" version="1.15.0">
-     <description>Trim sequences - primers, barcodes, quality</description>
-    </tool>
-    <tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.15.0">
-     <description>Describes whether two or more communities have the same structure</description>
+    <tool id="mothur_summary_single" name="Summary.single" version="1.16.0" force_history_refresh="True">
+     <description>Summary of calculator values for OTUs</description>
     </tool>
-    <tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.15.0">
-     <description>Describes whether two or more communities have the same structure</description>
-    </tool>
-    <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.15.0">
-     <description>Return unique sequences</description>
-    </tool>
-    <tool id="mothur_venn" name="Venn" version="1.15.0" >
-     <description>Generate Venn diagrams gor groups </description>
+    <tool id="mothur_tree_shared" name="Tree.shared" version="1.16.0" force_history_refresh="True">
+     <description>Generate a newick tree for dissimilarity among groups</description>
     </tool>
     <tool id="tree_vector" name="TreeVector" version="1.0">
      <description>Draw a Phylogenic Tree</description>
     </tool>
+    <tool id="mothur_trim_seqs" name="Trim.seqs" version="1.16.0">
+     <description>Trim sequences - primers, barcodes, quality</description>
+    </tool>
+    <tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.16.0">
+     <description>Describes whether two or more communities have the same structure</description>
+    </tool>
+    <tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.16.0">
+     <description>Describes whether two or more communities have the same structure</description>
+    </tool>
+    <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.16.0">
+     <description>Return unique sequences</description>
+    </tool>
+    <tool id="mothur_venn" name="Venn" version="1.16.0"  force_history_refresh="True">
+     <description>Generate Venn diagrams gor groups </description>
+    </tool>
 </suite>