Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/README @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
| author | certain cat |
|---|---|
| date | Fri, 31 Oct 2014 15:09:32 -0400 |
| parents | 49058b1f8d3f |
| children | 040410b8167e |
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--- a/mothur/README Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/README Fri Oct 31 15:09:32 2014 -0400 @@ -1,15 +1,27 @@ Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page + Mothur should be able to be auto-installed as a tool_dependency You may want to reorganize the tool panel after installing See below: Reorganize integrated_tool_panel.xml This was based on: http://www.mothur.org/wiki/Mothur_manual (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used for mothur commands) This will be set in: tool_dependencies/mothur/1.27/jjohnson/mothur_toolsuite/*/env.sh + Requirements for auto installation: + - make (sudo-apt get install make) + - g++ (sudo apt-get install g++) + - gfortran (sudo apt-get install gfortran) + - pip (sudo apt-get install python-pip) + - simplejson (pip install simplejson) + + Repository Dependency: + - BLAST Legacy ver. 2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/) + - The repository name should be package_blast_2_2_26 so it matches with the tool dependency. + Manual installation for Mothur: - Install mothur v.1.27 on your galaxy system so galaxy can execute the mothur command - ( This version of wrappers is designed for Mothur version 1.27 - it may work on later versions ) + Install mothur v.1.33 on your galaxy system so galaxy can execute the mothur command + ( This version of wrappers is designed for Mothur version 1.33- it may work on later versions ) http://www.mothur.org/wiki/Download_mothur http://www.mothur.org/wiki/Installation ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) @@ -126,292 +138,8 @@ add datatypes to: datatypes_conf.xml - <!-- Start Mothur Datatypes --> - <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/> - <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/> - <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/> - <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/> - <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/> - <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/> - <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/> - <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/> - <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/> - <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/> - <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/> - <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/> - <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/> - <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/> - <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/> - <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/> - <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/> - <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/> - <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/> - <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/> - <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/> - <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true"> - <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/> - </datatype> - <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/> - <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/> - <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/> - <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/> - <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/> - <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/> - <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/> - <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/> - <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/> - <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/> - <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/> - <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="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_files/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_files/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_groups/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_groups/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_groups/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_groups/1.22.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_design/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sub_sample/1.22.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sort_seqs/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_create_database/1.27.0" /> - <tool id="toolshed.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="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sffinfo/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_flows/1.26.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_flows/1.22.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_seqs/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_contigs/1.26.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_fastq/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_fastq_info/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_qual/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_reverse_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcr_seqs/1.25.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_seqs/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unique_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chop_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_screen_seqs/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_filter_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_degap_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_consensus_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_check/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pairwise_seqs/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_abund/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_groups/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcoa/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pca/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_nmds/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_corr_axes/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_seqs/1.21.0" /> - <tool id="toolshed.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="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_bellerophon/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_ccode/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_check/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_perseus/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_pintail/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_slayer/1.22.0" /> - <tool id="toolshed.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="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pre_cluster/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_fragments/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster/1.27.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_hcluster/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_classic/1.27.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_split/1.27.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_metastats/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sens_spec/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_otu/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parse_list/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otus/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otus/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_rare/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulist/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_oturep/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_otulabels/1.26.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulabels/1.26.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otulabels/1.26.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_hierarchy/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_rabund/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sabund/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_relabund/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared/1.22.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared_from_biom/1.25.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_biom/1.25.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_group/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_bin_seqs/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sharedseqs/1.20.0" /> - <tool id="toolshed.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="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_single/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_single/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_single/1.19.0" /> - <tool id="toolshed.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="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_shared/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_shared/1.26.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_normalize_shared/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_shared/1.26.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_association/1.24.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_shared/1.25.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_sim/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_venn/1.23.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_tree_shared/1.25.0" /> - <tool id="toolshed.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="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parsimony/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_weighted/1.25.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_unweighted/1.25.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_libshuff/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_amova/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_homova/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_mantel/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_anosim/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cooccurrence/1.25.0" /> - <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_lineage/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_lineage/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylotype/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylo_diversity/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_clearcut/1.19.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_indicator/1.21.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_tree/1.20.0" /> - <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_tree/1.24.0" /> - <tool id="toolshed.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"/> - <tool file="mothur/merge.files.xml"/> - <tool file="mothur/make.group.xml"/> - <tool file="mothur/get.groups.xml"/> - <tool file="mothur/remove.groups.xml"/> - <tool file="mothur/merge.groups.xml"/> - <tool file="mothur/count.groups.xml"/> - <tool file="mothur/make.design.xml"/> - <tool file="mothur/sub.sample.xml"/> - <tool file="mothur/sort.seqs.xml"/> - <tool file="mothur/create.database.xml"/> - <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> - <tool file="mothur/sffinfo.xml"/> - <tool file="mothur/trim.flows.xml"/> - <tool file="mothur/shhh.flows.xml"/> - <tool file="mothur/shhh.seqs.xml"/> - <tool file="mothur/make.fastq.xml"/> - <tool file="mothur/fastq.info.xml"/> - <tool file="mothur/summary.seqs.xml"/> - <tool file="mothur/summary.qual.xml"/> - <tool file="mothur/count.seqs.xml"/> - <tool file="mothur/reverse.seqs.xml"/> - <tool file="mothur/list.seqs.xml"/> - <tool file="mothur/get.seqs.xml"/> - <tool file="mothur/remove.seqs.xml"/> - <tool file="mothur/trim.seqs.xml"/> - <tool file="mothur/pcr.seqs.xml"/> - <tool file="mothur/unique.seqs.xml"/> - <tool file="mothur/deunique.seqs.xml"/> - <tool file="mothur/chop.seqs.xml"/> - <tool file="mothur/screen.seqs.xml"/> - <tool file="mothur/filter.seqs.xml"/> - <tool file="mothur/degap.seqs.xml"/> - <tool file="mothur/consensus.seqs.xml"/> - <tool file="mothur/align.seqs.xml"/> - <tool file="mothur/align.check.xml"/> - <tool file="mothur/dist.seqs.xml"/> - <tool file="mothur/pairwise.seqs.xml"/> - <tool file="mothur/split.abund.xml"/> - <tool file="mothur/split.groups.xml"/> - <tool file="mothur/pcoa.xml"/> - <tool file="mothur/pca.xml"/> - <tool file="mothur/nmds.xml"/> - <tool file="mothur/corr.axes.xml"/> - <tool file="mothur/classify.seqs.xml"/> - <tool file="mothur/seq.error.xml"/> - <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/> - <tool file="mothur/chimera.bellerophon.xml"/> - <tool file="mothur/chimera.ccode.xml"/> - <tool file="mothur/chimera.check.xml"/> - <tool file="mothur/chimera.perseus.xml"/> - <tool file="mothur/chimera.pintail.xml"/> - <tool file="mothur/chimera.slayer.xml"/> - <tool file="mothur/chimera.uchime.xml"/> - <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/> - <tool file="mothur/pre.cluster.xml"/> - <tool file="mothur/cluster.fragments.xml"/> - <tool file="mothur/cluster.xml"/> - <tool file="mothur/hcluster.xml"/> - <tool file="mothur/cluster.classic.xml"/> - <tool file="mothur/cluster.split.xml"/> - <tool file="mothur/metastats.xml"/> - <tool file="mothur/sens.spec.xml"/> - <tool file="mothur/classify.otu.xml"/> - <tool file="mothur/parse.list.xml"/> - <tool file="mothur/get.otus.xml"/> - <tool file="mothur/remove.otus.xml"/> - <tool file="mothur/remove.rare.xml"/> - <tool file="mothur/get.otulist.xml"/> - <tool file="mothur/get.oturep.xml"/> - <tool file="mothur/otu.hierarchy.xml"/> - <tool file="mothur/get.rabund.xml"/> - <tool file="mothur/get.sabund.xml"/> - <tool file="mothur/get.relabund.xml"/> - <tool file="mothur/make.shared.xml"/> - <tool file="mothur/make.shared_from_biom.xml"/> - <tool file="mothur/make.biom.xml"/> - <tool file="mothur/get.group.xml"/> - <tool file="mothur/bin.seqs.xml"/> - <tool file="mothur/get.sharedseqs.xml"/> - <tool file="mothur/summary.tax.xml"/> - <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> - <tool file="mothur/collect.single.xml"/> - <tool file="mothur/rarefaction.single.xml"/> - <tool file="mothur/summary.single.xml"/> - <tool file="mothur/heatmap.bin.xml"/> - <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/> - <tool file="mothur/collect.shared.xml"/> - <tool file="mothur/rarefaction.shared.xml"/> - <tool file="mothur/normalize.shared.xml"/> - <tool file="mothur/summary.shared.xml"/> - <tool file="mothur/otu.association.xml"/> - <tool file="mothur/dist.shared.xml"/> - <tool file="mothur/heatmap.sim.xml"/> - <tool file="mothur/venn.xml"/> - <tool file="mothur/tree.shared.xml"/> - <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/> - <tool file="mothur/parsimony.xml"/> - <tool file="mothur/unifrac.weighted.xml"/> - <tool file="mothur/unifrac.unweighted.xml"/> - <tool file="mothur/libshuff.xml"/> - <tool file="mothur/amova.xml"/> - <tool file="mothur/homova.xml"/> - <tool file="mothur/mantel.xml"/> - <tool file="mothur/anosim.xml"/> - <tool file="mothur/cooccurrence.xml"/> - <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> - <tool file="mothur/get.lineage.xml"/> - <tool file="mothur/remove.lineage.xml"/> - <tool file="mothur/phylotype.xml"/> - <tool file="mothur/phylo.diversity.xml"/> - <tool file="mothur/clearcut.xml"/> - <tool file="mothur/indicator.xml"/> - <tool file="mothur/deunique.tree.xml"/> - <tool file="mothur/classify.tree.xml"/> - <tool file="mothur/TreeVector.xml"/> - </section> <!-- metagenomics_mothur --> ############ DESIGN NOTES ######################################################################################################### Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py