Mercurial > repos > jjohnson > mothur_toolsuite

changeset 14:216bf44bf185 draft default tip

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Update README with suggested tool_panael layout
author Jim Johnson <jj@umn.edu>
date Tue, 04 Dec 2012 09:56:39 -0600
parents 729e90f1e874
children
files mothur/README mothur/tools/suite_config.xml
diffstat 2 files changed, 128 insertions(+), 237 deletions(-) [+]
line wrap: on
line diff
--- a/mothur/README	Mon Dec 03 09:09:43 2012 -0600
+++ b/mothur/README	Tue Dec 04 09:56:39 2012 -0600
@@ -160,6 +160,134 @@
         <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
         <!-- End Mothur Datatypes -->
 
+Reorganize integrated_tool_panel.xml :
+    <section id="metagenomics_mothur" name="Metagenomics Mothur" version="">
+      <label text="Mothur Utilities" id="mothur_utilities"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_files/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_files/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_groups/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_groups/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_groups/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_groups/1.22.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_design/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sub_sample/1.22.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sort_seqs/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_create_database/1.27.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/CONVERTER_ref_to_seq_taxomony/1.0.0" />
+      <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sffinfo/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_flows/1.26.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_flows/1.22.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_seqs/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_contigs/1.26.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_fastq/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_fastq_info/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_qual/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_reverse_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcr_seqs/1.25.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_seqs/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unique_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chop_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_screen_seqs/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_filter_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_degap_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_consensus_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_check/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pairwise_seqs/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_abund/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_groups/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcoa/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pca/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_nmds/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_corr_axes/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_seqs/1.21.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_seq_error/1.22.0" />
+      <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_bellerophon/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_ccode/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_check/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_perseus/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_pintail/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_slayer/1.22.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_uchime/1.22.0" />
+      <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pre_cluster/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_fragments/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster/1.27.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_hcluster/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_classic/1.27.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_split/1.27.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_metastats/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sens_spec/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_otu/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parse_list/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otus/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otus/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_rare/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulist/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_oturep/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_otulabels/1.26.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulabels/1.26.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otulabels/1.26.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_hierarchy/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_rabund/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sabund/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_relabund/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared/1.22.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared_from_biom/1.25.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_biom/1.25.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_group/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_bin_seqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sharedseqs/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_tax/1.22.0" />
+      <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_single/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_single/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_single/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_bin/1.20.0" />
+      <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_shared/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_shared/1.26.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_normalize_shared/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_shared/1.26.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_association/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_shared/1.25.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_sim/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_venn/1.23.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_tree_shared/1.25.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_coremicrobiome/1.26.0" />
+      <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parsimony/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_weighted/1.25.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_unweighted/1.25.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_libshuff/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_amova/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_homova/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_mantel/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_anosim/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cooccurrence/1.25.0" />
+      <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_lineage/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_lineage/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylotype/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylo_diversity/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_clearcut/1.19.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_indicator/1.21.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_tree/1.20.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_tree/1.24.0" />
+        <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/tree_vector/1.0" />
+    </section>
+
+
+
 add mothur tools to:   tool_conf.xml
   <section name="Metagenomics Mothur" id="metagenomics_mothur">
     <label text="Mothur Utilities" id="mothur_utilities"/>
--- a/mothur/tools/suite_config.xml	Mon Dec 03 09:09:43 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,237 +0,0 @@
-<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="1.16.0">
- <description>Align sequences to a template alignment</description>
-</tool>
-<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_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="1.16.0">
- <description>Find putative chimeras using ccode</description>
-</tool>
-<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="1.16.0">
- <description>Find putative chimeras using pintail</description>
-</tool>
-<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="1.16.0">
- <description>Trim sequences to a specified length</description>
-</tool>
-<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="1.16.0">
- <description>Assign sequences to taxonomy</description>
-</tool>
-<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="1.16.0">
- <description>Assign sequences to OTUs (Dotur implementation)</description>
-</tool>
-<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_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="1.16.0" force_history_refresh="True">
- <description>Generate collector's curves for calculators on OTUs</description>
-</tool>
-<tool id="mothur_collect_single" name="Collect.single" version="1.16.0" force_history_refresh="True">
- <description>Summary of calculator values for OTUs</description>
-</tool>
-<tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.16.0" force_history_refresh="True">
- <description>Find a consensus sequence for each OTU or phylotype</description>
-</tool>
-<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="1.16.0">
- <description>Return all sequences</description>
-</tool>
-<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="1.16.0" 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="1.16.0">
- <description>Convert fastq to fasta and quality</description>
-</tool>
-<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="1.16.0">
- <description>Select groups</description>
-</tool>
-<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="1.16.0"  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="1.16.0">
- <description>Get otus containing sequences from specified groups</description>
-</tool>
-<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="1.16.0">
- <description>Picks sequences by name</description>
-</tool>
-<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="1.16.0"  force_history_refresh="True">
- <description>Generate a heatmap for OTUs</description>
-</tool>
-<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="1.16.0">
- <description>Identify indicator "species" for nodes on a tree</description>
-</tool>
-<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="1.16.0">
- <description>Lists the names of the sequences</description>
-</tool>
-<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="1.16.0">
- <description>Merge data</description>
-</tool>
-<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="1.16.0">
- <description>calculate uncorrected pairwise distances between sequences</description>
-</tool>
-<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="1.16.0">
- <description>Describes whether two or more communities have the same structure</description>
-</tool>
-<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="1.16.0">
- <description>Alpha Diversity calculate unique branch length</description>
-</tool>
-<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="1.16.0">
- <description>Remove sequences due to pyrosequencing errors</description>
-</tool>
-<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="1.16.0" force_history_refresh="True">
- <description>Generate intra-sample rarefaction curves for OTUs</description>
-</tool>
-<tool id="mothur_read_otu" name="Read.otu" version="1.16.0" 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="1.16.0">
- <description>Remove groups</description>
-</tool>
-<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="1.16.0">
- <description>Remove otus containing sequences from specified groups</description>
-</tool>
-<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="1.16.0">
- <description>Reverse complement the sequences</description>
-</tool>
-<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.16.0">
- <description>Screen sequences</description>
-</tool>
-<tool id="mothur_sffinfo" name="Sffinfo" version="1.16.0">
- <description>Summarize the quality of sequences</description>
-</tool>
-<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="1.16.0" force_history_refresh="True">
- <description>Generates a fasta file for each group</description>
-</tool>
-<tool id="mothur_sub_sample" name="Sub.sample" version="1.16.0">
- <description>Create a sub sample</description>
-</tool>
-<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="1.16.0"  force_history_refresh="True">
- <description>Summary of calculator values for OTUs</description>
-</tool>
-<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_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>