Mercurial > repos > jjohnson > mothur_toolsuite
changeset 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
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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" /> - 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<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
--- a/mothur/datatypes_conf.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/datatypes_conf.xml Fri Oct 31 15:09:32 2014 -0400 @@ -50,6 +50,8 @@ <datatype extension="nhx" type="galaxy.datatypes.metagenomics:Nhx" display_in_upload="true"/> <datatype extension="nex" type="galaxy.datatypes.metagenomics:Nexus" display_in_upload="true"/> <datatype extension="count_table" type="galaxy.datatypes.metagenomics:CountTable" display_in_upload="true"/> + <datatype extension="otu_map" type="galaxy.datatypes.metagenomics:OtuMap" display_in_upload="true"/> + <datatype extension="metadata" type="galaxy.datatypes.metagenomics:Metadata" display_in_upload="true"/> <!-- End Mothur Datatypes --> <!-- Start Qiime Datatypes --> <datatype extension="qiimemapping" type="galaxy.datatypes.metagenomics:QiimeMetadataMapping" display_in_upload="true"/> @@ -75,6 +77,8 @@ <sniffer type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix"/> <sniffer type="galaxy.datatypes.metagenomics:Oligos"/> <sniffer type="galaxy.datatypes.metagenomics:Frequency"/> + <sniffer type="galaxy.datatypes.metagenomics:OtuMap"/> + <sniffer type="galaxy.datatypes.metagenomics:Metadata"/> <sniffer type="galaxy.datatypes.metagenomics:Quantile"/> <sniffer type="galaxy.datatypes.metagenomics:LaneMask"/> <sniffer type="galaxy.datatypes.metagenomics:RefTaxonomy"/>
--- a/mothur/lib/galaxy/datatypes/metagenomics.py Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/lib/galaxy/datatypes/metagenomics.py Fri Oct 31 15:09:32 2014 -0400 @@ -22,6 +22,7 @@ ## Mothur Classes class Otu( Text ): + file_ext = 'otu' MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 ) MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] ) @@ -752,6 +753,127 @@ finally: fh.close() return False +""" +class OtuMap( Tabular ): + file_ext = 'otu_map' + + def __init__(self, **kwd): + Tabular.__init__(self,**kwd) + self.column_names = ['catdog','dog'] + self.column_types = ['int','float'] + + def sniff(self, filename): #sniffer that detects whether it's an otu table. + #it appears that self refers to the object passed in, and filename will be the name of the file? + try: + fh = open( filename) + line = fh.readline() + line = line.strip() + if line[0] != '#': + return False + count=0 + while True: + #go thru the file. + line = fh.readline() + line = line.strip() + if not line: + break + else: + if line[0] != '#': + try: + linePieces = line.split('\t') + i = int(linePieces[0]) + f = float(linePieces[1]) + continue + except: + return False + #went through the file, can split! + return True + except: + #failed to open file ? + pass + finally: + fh.close() + #at this point we might as well return false.. + return False +""" +class Metadata ( Tabular ): + file_ext='metadata' + """ + group dpw description + F003D000 0 "F003D000 description" + F003D002 2 "F003D002 description" + F003D004 4 "F003D004 description" + F003D006 6 "F003D006 description" + F003D008 8 "F003D008 description" + F003D142 142 "F003D142 description" + F003D144 144 "F003D144 description" + F003D146 146 "F003D146 description" + F003D148 148 "F003D148 description" + F003D150 150 "F003D150 description" + MOCK.GQY1XT001 12 "MOCK.GQY1XT001 description" + """ + def __init__(self, **kwd): + Tabular.__init__( self, **kwd ) + self.column_names = ['group','dpw','description'] + self.column_types = ['string','int','string'] + + def sniff (self,filename): + try: + fh = open (filename) + line = fh.readline() + line = line.strip() + headers = line.split('\t') + #check the header for the needed + if headers[0] == "group" and headers[1] == "dpw" and headers[2] == "description": + return True + except: + pass + finally: + fh.close() + return False + + + +class OtuMap(Tabular): + file_ext = 'otu_map' + def __init__(self, **kwd): + """A list of names""" + Tabular.__init__( self, **kwd ) + self.column_names = ['OTU','SEQIDS'] + self.column_types = ['int','float'] + + def sniff( self, filename ): + """ + Determines whether the file is a frequency tabular format for chimera analysis + #1.14.0 + 0 0.000 + 1 0.000 + ... + 155 0.975 + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + else: + if line[0] != '#': + try: + linePieces = line.split('\t') + i = int(linePieces[0]) + continue + except: + return False + return True + except: + pass + finally: + fh.close() + return False + class Frequency(Tabular): file_ext = 'freq' @@ -772,6 +894,11 @@ """ try: fh = open( filename ) + #checks first line for # + line = fh.readline() + line = line.strip() + if line[0] != '#': + return False count = 0 while True: line = fh.readline() @@ -1400,7 +1527,6 @@ fh.close() return False - ## Biom class BiologicalObservationMatrix( Text ):
--- a/mothur/tool-data/datatypes.conf.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tool-data/datatypes.conf.xml Fri Oct 31 15:09:32 2014 -0400 @@ -39,6 +39,7 @@ <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="otu_map" type="galaxy.datatypes.metagenomics:OtuMap" 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"/> @@ -75,6 +76,7 @@ <sniffer type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix"/> <sniffer type="galaxy.datatypes.metagenomics:Oligos"/> <sniffer type="galaxy.datatypes.metagenomics:Frequency"/> + <sniffer type="galaxy.datatypes.metagenomics:OtuMap"/> <sniffer type="galaxy.datatypes.metagenomics:Quantile"/> <sniffer type="galaxy.datatypes.metagenomics:LaneMask"/> <sniffer type="galaxy.datatypes.metagenomics:RefTaxonomy"/>
--- a/mothur/tool_dependencies.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tool_dependencies.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,44 +1,122 @@ -<?xml version="1.0"?> +<?eml version="1.0"?> <tool_dependency> - <package name="mothur" version="1.27"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action> - <!-- Update the makefile --> - <action type="shell_command">sed -i 's/^USECOMPRESSION ?= no/USECOMPRESSION ?= yes/' Mothur.source/makefile</action> - <action type="shell_command">sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' Mothur.source/makefile</action> - <action type="shell_command">sed -i 's/#CXXFLAGS +=/CXXFLAGS +=/' Mothur.source/makefile</action> - <!-- Update the uchime_src/mk --> - <action type="shell_command">sed -i 's/LINK_OPTS=-static/LINK_OPTS=/' Mothur.source/uchime_src/mk</action> - <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> - <action type="shell_command">cd Mothur.source && make</action> - <action type="move_file"> - <source>Mothur.source/mothur</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>Mothur.source/uchime</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable> - </action> - </actions> - </install> - <readme> -These links provide information for building the Mothur package in most environments . + <!-- + <package name="mothur" version="1.27"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action> + <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> + <action type="shell_command"> + test $(uname) = Linux && + perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile || + true + </action> + <action type="shell_command">cd Mothur.source; make -j 2;</action> + <action type="move_file"> + <source>Mothur.source/mothur</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>Mothur.source/uchime</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable> + </action> + </actions> + </install> + <readme> + + Iyad Kandalaft added shell commands to build in Linux environment such as Redhat/Centos/Ubuntu. ReadLine libraries are not required. libncurses-devel are required. + + These links provide information for building the Mothur package in most environments . + + http://www.mothur.org/wiki/Download_mothur + + http://www.mothur.org/wiki/Installation + + http://www.mothur.org/wiki/Makefile_options -http://www.mothur.org/wiki/Download_mothur - -http://www.mothur.org/wiki/Installation - -http://www.mothur.org/wiki/Makefile_options + </readme> + </package> +--> + <package name="mothur" version="1.33"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://www.mothur.org/w/images/6/65/Mothur.1.33.3.zip</action> + <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> + <!-- + <action type="shell_command"> + test -e /etc/redhat-release && + perl -i.bak -pe 's/#(CXX.+g\+\+44)/$1/;' Mothur.source/makefile || + true + </action> + --> + <action type="shell_command"> + test $(uname) = Linux && + perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile || + true + </action> + <action type="shell_command">cd Mothur.source; make -j 2;</action> + <action type="move_file"> + <source>Mothur.source/mothur</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>Mothur.source/uchime</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable> + </action> + <action type="set_environment_for_install"> + <repository changeset_revision="32c158152e5e" name="package_blast_plus_2_2_26" owner="meowmeow" toolshed="http://onotta669816x:9001/"> + <package name="blast" version="2.2.26" /> + </repository> + </action> - </readme> - </package> - <!-- - http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip - --> -</tool_dependency> + <!-- + <action type="shell_command">mkdir $INSTALL_DIR/bin/blast; mkdir $INSTALL_DIR/bin/blast/bin;</action> + --> + <action type="make_directory">$INSTALL_DIR/bin/blast</action> + <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action> + <action type="change_directory">$INSTALL_DIR/bin</action> + <!-- + <action type="shell_command">cd $INSTALL_DIR/bin; cp ../../../../../../blast/*/*/package_blast_plus_2_2_26/*/* ./blast/bin</action> + --> + + <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action> + + </actions> + </install> + <readme> + + Iyad Kandalaft added shell commands to build in Linux environment such as Redhat/Centos/Ubuntu. ReadLine libraries are not required. libncurses-devel are required. + + These links provide information for building the Mothur package in most environments . + + http://www.mothur.org/wiki/Download_mothur + http://www.mothur.org/wiki/Installation + + http://www.mothur.org/wiki/Makefile_options + + </readme> + </package> + <!-- + http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip + --> + + <package name="blast" version="2.2.26"> + <repository + name="package_blast_plus_2_2_26" + owner="meowmeow" + changeset_revision="32c158152e5e" + toolshed="http://onotta669816x:9001/" + prior_installation_required="True"/> + </package> + + </tool_dependency> +
--- a/mothur/tools/mothur/align.check.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/align.check.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_align_check" name="Align.check" version="1.19.0"> +<tool id="mothur_align_check" name="Align.check" version="1.20.0"> <description>Calculate the number of potentially misaligned bases</description> <command interpreter="python"> mothur_wrapper.py @@ -6,7 +6,14 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file --outputdir='$logfile.extra_files_path' --fasta=$fasta - --map=$ss.map + --map=$ss.map + #if $count.__str__ != "None" and len($count.__str__) >0: + --count=$count + #end if + #if $count.__str__ != "None" and len($count.__str__) >0: + --name=$name + #end if + </command> <inputs> <param name="fasta" type="data" format="align" label="fasta - Aligned Sequences"/> @@ -17,23 +24,23 @@ </param> <when value="cached"> <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions"> - <options from_file="mothur_map.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_map"> </options> </param> </when> <when value="history"> <param name="map" format="map" type="data" label="Secondary Structure Map" /> </when> - </conditional> + </conditional> + <param name="count" type="data" format="count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/> + <param name="name" type="data" format="names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/align.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/align.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_align_seqs" name="Align.seqs" version="1.19.0"> +<tool id="mothur_align_seqs" name="Align.seqs" version="1.20.0"> <description>Align sequences to a template alignment</description> <command interpreter="python"> mothur_wrapper.py @@ -34,9 +34,7 @@ </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_aligndb"> </options> </param> </when> @@ -96,7 +94,7 @@ <data format="align.report" name="report" label="${tool.name} on ${on_string}: align.report" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/amova.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/amova.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_amova" name="Amova" version="1.19.0"> +<tool id="mothur_amova" name="Amova" version="1.20.0"> <description>Analysis of molecular variance</description> <command interpreter="python"> mothur_wrapper.py @@ -12,21 +12,29 @@ #end if #if float($alpha.__str__) > 0.0: --alpha=$alpha - #end if + #end if + #if $sets.__str__ != "None" and len ($sets.__str__) >0: + --sets=$sets + #end if </command> <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design) "/> <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> - <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> + <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> + <param name="sets" type="select" label="sets - Which of the sets in your design file you would like to analyze. The set names are separated by dashes. The defualt is all sets in designfile" multiple = "true"> + <options> + <filter type="data_meta" ref="design" key="sets"/> + </options> + </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="amova" label="${tool.name} on ${on_string}: amova"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/anosim.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/anosim.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_anosim" name="Anosim" version="1.19.0"> +<tool id="mothur_anosim" name="Anosim" version="1.20.0"> <description>Non-parametric multivariate analysis of changes in community structure</description> <command interpreter="python"> mothur_wrapper.py @@ -26,7 +26,7 @@ <data format="tabular" name="anosim" label="${tool.name} on ${on_string}: anosim"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/bin.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/bin.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,58 +1,63 @@ -<tool id="mothur_bin_seqs" name="Bin.seqs" version="1.20.0" force_history_refresh="True"> - <description>Order Sequences by OTU</description> - <command interpreter="python"> - mothur_wrapper.py - --cmd='bin.seqs' - --result='^mothur.\S+\.logfile$:'$logfile - --outputdir='$logfile.extra_files_path' - --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}' - --fasta=$fasta - --list=$otu - #if $name.__str__ != "None" and len($name.__str__) > 0: - --name=$name - #end if - #if $label.__str__ != "None" and len($label.__str__) > 0: - --label='$label' - #end if - #if $group.__str__ != "None" and len($group.__str__) > 0: - --group='$group' - #end if - </command> - <inputs> - <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> - <param name="otu" type="data" format="list" label="list - OTU List"/> - <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> - <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options> - <filter type="data_meta" ref="otu" key="labels" /> - </options> - </param> - <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> - </inputs> - <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - </outputs> - <requirements> - <requirement type="package" version="1.27">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** +<tool id="mothur_bin_seqs" name="Bin.seqs" version="1.21.0" force_history_refresh="True"> + <description>Order Sequences by OTU</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='bin.seqs' + --result='^mothur.\S+\.logfile$:'$logfile + --outputdir='$logfile.extra_files_path' + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}' + --fasta=$fasta + --list=$otu + #if $name.__str__ != "None" and len($name.__str__) > 0: + --name=$name + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label='$label' + #end if + #if $group.__str__ != "None" and len($group.__str__) > 0: + --group='$group' + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count='$count' + #end if -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. - -.. _Mothur: http://www.mothur.org/wiki/Main_Page - -**Command Documenation** + </command> + <inputs> + <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> + <param name="otu" type="data" format="list" label="list - OTU List"/> + <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> + <param name="label" type="select" label="label - OTU Labels" multiple="true"> + <options> + <filter type="data_meta" ref="otu" key="labels" /> + </options> + </param> + <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> + <param name="count" type="data" format="count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + </outputs> + <requirements> + <requirement type="package" version="1.33">mothur</requirement> + </requirements> + <tests> + </tests> + <help> + **Mothur Overview** -The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. + Mothur_, initiated by Dr. Patrick Schloss and his software development team + in the Department of Microbiology and Immunology at The University of Michigan, + provides bioinformatics for the microbial ecology community. + + .. _Mothur: http://www.mothur.org/wiki/Main_Page + + **Command Documenation** -.. _list_file: http://www.mothur.org/wiki/List_file -.. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs + The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. - </help> + .. _list_file: http://www.mothur.org/wiki/List_file + .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs + + </help> </tool>
--- a/mothur/tools/mothur/chimera.bellerophon.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.bellerophon.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chimera_bellerophon" name="Chimera.bellerophon" version="1.20.0"> +<tool id="mothur_chimera_bellerophon" name="Chimera.bellerophon" version="1.21.0"> <description>Find putative chimeras using bellerophon</description> <command interpreter="python"> mothur_wrapper.py @@ -31,7 +31,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: bellerophon.accnos" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.ccode.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.ccode.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.20.0"> +<tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.21.0"> <description>Find putative chimeras using ccode</description> <command interpreter="python"> mothur_wrapper.py @@ -30,9 +30,7 @@ </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_aligndb"> </options> </param> </when> @@ -64,7 +62,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: ccode.accnos" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.check.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.check.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chimera_check" name="Chimera.check" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_chimera_check" name="Chimera.check" version="1.21.0" force_history_refresh="True"> <description>Find putative chimeras using chimeraCheck</description> <command interpreter="python"> mothur_wrapper.py @@ -34,9 +34,7 @@ </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_aligndb"> </options> </param> </when> @@ -64,7 +62,7 @@ <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.chimeras" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.perseus.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.perseus.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.23.0" > +<tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.24.0" > <description>Find putative chimeras using chimeraCheck</description> <command interpreter="python"> mothur_wrapper.py @@ -7,7 +7,11 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos --outputdir='$logfile.extra_files_path' --fasta=$fasta - --name=$name + #if isinstance($name.datatype, $__app__.datatypes_registry.get_datatype_by_extension('name').__class__): + --name=$name + #else + --count=$name + #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group='$group' #end if @@ -21,14 +25,16 @@ --cutoff=$cutoff #end if --processors=8 + $dereplicate </command> <inputs> <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> - <param name="name" type="data" format="names" label="name - Names "/> + <param name="name" type="data" format="names,count" label="name - Names or count_table"/> <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/> <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/> <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> + <param name="dereplicate" type="boolean" falsevalue="" truevalue="--dereplicate=true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -36,7 +42,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: perseus.accnos" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.pintail.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.pintail.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.20.0"> +<tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.21.0"> <description>Find putative chimeras using pintail</description> <command interpreter="python"> mothur_wrapper.py @@ -44,9 +44,7 @@ </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_aligndb"> </options> </param> </when> @@ -122,7 +120,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.slayer.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.slayer.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.22.0"> +<tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.23.0"> <description>Find putative chimeras using slayer</description> <command interpreter="python"> mothur_wrapper.py @@ -14,7 +14,10 @@ #end if #if $alignment.group.__str__ != '': --group=$alignment.group - #end if + #end if + #if $alignment.count.__str__ != '': + --count=$alignment.count + #end if #else: --reference=$alignment.template #end if @@ -36,7 +39,8 @@ $options.split #end if ## --blastlocation=path_to_blast - --processors=8 + --processors=8 + $dereplicate </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> @@ -48,16 +52,15 @@ </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_aligndb"> </options> </param> </when> <when value="hist"> <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> - </when> - <when value="self"> + </when> + <when value="self"> + <param name="count" type="data" format="count_table" optional="true" label="count - Count file"/> <param name="name" type="data" format="names" optional="true" label="names - Sequences Names"/> <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference" help="use the more abundant sequences from the same sample to check the query sequence"/> @@ -90,7 +93,11 @@ <param name="trim" type="boolean" truevalue="--trim=True" falsevalue="" checked="false" label="trim - include chimeric sequences trimmed to their longest peice" /> <param name="split" type="boolean" truevalue="--split=True" falsevalue="" checked="false" label="split - detect tri- and quadmeras" help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/> </when> - </conditional> + </conditional> + + <param name="dereplicate" type="boolean" falsevalue="" truevalue="--dereplicate=true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/> + + </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -98,7 +105,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: slayer.accnos" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.uchime.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chimera.uchime.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chimera_uchime" name="Chimera.uchime" version="1.22.0"> +<tool id="mothur_chimera_uchime" name="Chimera.uchime" version="1.23.0"> <description>Find putative chimeras using uchime</description> <command interpreter="python"> mothur_wrapper.py @@ -26,6 +26,9 @@ #if $template.group.__str__ != '': --group=$template.group #end if + #if $template.count.__str__ != '': + --count=$template.count + #end if #elif $template.source == 'names': --name=$template.name #end if @@ -69,10 +72,11 @@ $skipgaps2 #if $alignment.ucl: --ucl=true - #if $alignment.queryfract != None and len($alignment.queryfract) > 0 and 1.0 >= float($alignment.queryfract) > 0: + #if $alignment.queryfract != "None" and len($alignment.queryfract) > 0 and 1.0 >= float($alignment.queryfract) > 0: --queryfract=$alignment.queryfract #end if #end if + $dereplicate $chimealns --processors=8 </command> @@ -87,9 +91,7 @@ </param> <when value="ref"> <param name="reference" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_aligndb"> </options> </param> </when> @@ -100,6 +102,8 @@ <param name="abskew" type="float" value="1.9" label="abskew - Abundance skew (default 1.9)" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query)"/> <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference" help="use the more abundant sequences from the same sample to check the query sequence"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" + help="Generated by count.seqs. When you use a count file with group info and dereplicate=T, mothur will create a *.pick.count_table file containing seqeunces after chimeras are removed."/> </when> <when value="names"> @@ -107,6 +111,8 @@ </when> </conditional> + <param name="dereplicate" type="boolean" falsevalue="" truevalue="--dereplicate=true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/> + <param name="minh" type="float" value="0.3" label="minh - mininum score to report chimera. Default 0.3" help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/> <param name="mindiv" type="float" value="0.5" label="mindiv - minimum divergence ratio, default 0.5" help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1"/> @@ -149,7 +155,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -168,6 +174,7 @@ .. _chimera.uchime: http://www.mothur.org/wiki/Chimera.uchime +Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options. </help> </tool>
--- a/mothur/tools/mothur/chop.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/chop.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_chop_seqs" name="Chop.seqs" version="1.19.0"> +<tool id="mothur_chop_seqs" name="Chop.seqs" version="1.20.0"> <description>Trim sequences to a specified length</description> <command interpreter="python"> mothur_wrapper.py @@ -10,7 +10,16 @@ --keep=$keep $countgaps $short - --processors=8 + --processors=8 + #if $name.__str__ != "None": + --name=$name + #end if + #if $group.__str__ != "None": + --group=$group + #end if + #if $count.__str__ != "None": + --count=$count + #end if </command> <inputs> <param name="fasta" type="data" format="fasta,align" label="fasta - Sequences to be chopped"/> @@ -21,13 +30,16 @@ </param> <param name="countgaps" type="boolean" truevalue="--countgaps=true" falsevalue="" checked="false" label="countgaps - Count gaps as bases"/> <param name="short" type="boolean" truevalue="--short=true" falsevalue="" checked="false" label="short - keep sequences that are too short to chop"/> + <param name="name" type="data" format="name" label="name file" optional="true"/> + <param name="group" type="data" format="group" label="group file" optional="true"/> + <param name="count" type="data" format="count_table" label="count file" optional = "true"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -46,6 +58,7 @@ .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs +v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0 </help> </tool>
--- a/mothur/tools/mothur/classify.otu.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/classify.otu.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_classify_otu" name="Classify.otu" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_classify_otu" name="Classify.otu" version="1.21.0" force_history_refresh="True"> <description>Assign sequences to taxonomy</description> <command interpreter="python"> mothur_wrapper.py @@ -12,7 +12,10 @@ #if $name.__str__ != "None" and len($name.__str__) > 0: --name='$name' #end if - #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count='$count' + #end if + #if $reftax.source != 'None' and len($reftax.taxonomy.__str__) > 0: --reftaxonomy=$reftax.taxonomy #end if #if 100 >= int($cutoff.__str__) > 0: @@ -25,11 +28,13 @@ --group='$group' #end if --basis=$basis - $probs + $probs + $persample </command> <inputs> <param name="otu" type="data" format="list" label="list - OTU List "/> <param name="name" type="data" format="names" optional="true" label="name - taxonomy sequence names"/> + <param name="count" type="data" format="count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/> <conditional name="tax"> <param name="source" type="select" label="Select Taxonomy from" help=""> <option value="hist">History</option> @@ -37,9 +42,7 @@ </param> <when value="ref"> <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"> - <options from_file="mothur_taxonomy.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_taxonomy"> </options> </param> </when> @@ -49,16 +52,14 @@ </conditional> <conditional name="reftax"> <param name="source" type="select" label="Select Reference Taxonomy used in Classify.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static."> - <option value="none">Selection is Optional</option> + <option value="None">Selection is Optional</option> <option value="hist">History</option> <option value="ref">Cached Reference</option> </param> - <when value="none"/> + <when value="None"/> <when value="ref"> <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"> - <options from_file="mothur_taxonomy.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_taxonomy"> </options> </param> </when> @@ -80,12 +81,13 @@ <option value="sequence">sequence</option> </param> <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/> + <param name="persample" type="boolean" falsevalue="" truevalue="--persample=true" checked="false" label="persample - allows you to find a consensus taxonomy for each group. default=f"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -106,6 +108,6 @@ .. _classify.otu: http://www.mothur.org/wiki/Classify.otu - +v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0) </help> </tool>
--- a/mothur/tools/mothur/classify.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/classify.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,119 +1,125 @@ -<tool id="mothur_classify_seqs" name="Classify.seqs" version="1.21.0"> - <description>Assign sequences to taxonomy</description> - <command interpreter="python"> - mothur_wrapper.py - --cmd='classify.seqs' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy$:'$taxonomy_out,'^\S+\.tax\.summary$:'$tax_summary - --outputdir='$logfile.extra_files_path' - --fasta=$fasta - --reference=$alignment.template - --taxonomy=$tax.taxonomy - #if $classify.method == 'bayesian': - --method=$classify.method - #if 15 >= int($classify.ksize.__str__) >= 4: - --ksize=$classify.ksize - #end if - #if int($classify.iters.__str__) > 0: - --iters=$classify.iters - #end if - #if 100 >= int($classify.cutoff.__str__) > 0: - --cutoff=$classify.cutoff - #end if - $classify.probs - #elif $classify.method == 'knn': - --method=$classify.method - --numwanted=$classify.search.numwanted - #if $classify.search.algorithm == 'kmer': - --search=$classify.search.algorithm - --ksize=$classify.search.ksize - #elif $classify.search.algorithm == 'blast': - --search=$classify.search.algorithm - --match=$classify.search.match - --mismatch=$classify.search.mismatch - --gapopen=$classify.search.gapopen - --gapextend=$classify.search.gapextend - #elif $classify.knn.search == 'suffix': - --search=$classify.search.algorithm - #elif $classify.search.algorithm == 'distance': - --search=$classify.search.algorithm - #end if - #end if - --processors=8 - </command> - <inputs> - <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> - <conditional name="alignment"> - <param name="source" type="select" label="Select Reference Template from" help=""> - <option value="hist">History</option> - <option value="ref">Cached Reference</option> - </param> - <when value="ref"> - <param name="template" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> - </options> - </param> - </when> - <when value="hist"> - <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> - </when> - </conditional> - <conditional name="tax"> - <param name="source" type="select" label="Select Taxonomy from" help=""> - <option value="ref">Cached Reference</option> - <option value="hist">History</option> - </param> - <when value="ref"> - <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy reference"> - <options from_file="mothur_taxonomy.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> - </options> - </param> - </when> - <when value="hist"> - <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy reference"/> - </when> - </conditional> - <conditional name="classify"> - <param name="method" type="select" label="method - Select a classification method" help=""> - <option value="bayesian">Bayesian (default)</option> - <option value="knn">K-Nearest Neighbor (knn)</option> - </param> - <when value="bayesian"> - <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"> - <validator type="in_range" message="ksize - kmer length between 5 and 12" min="5" max="12"/> - </param> - <param name="iters" type="integer" value="100" label="iters - iterations to do when calculating the bootstrap confidence score"/> - <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"> - <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/> - </param> - <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/> - </when> - <when value="knn"> - <param name="numwanted" type="integer" value="10" label="numwanted - "/> - <conditional name="search"> - <param name="algorithm" type="select" label="algorithm - " help=""> - <option value="kmer">Kmer (default)</option> - <option value="blast">BLAST</option> - <option value="suffix">Suffix Tree</option> - <option value="distance">Distance</option> - </param> - <when value="kmer"> - <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"/> - </when> - <when value="blast"> - <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> - <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/> - <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> - <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/> - </when> - <when value="suffix"/> - <when value="distance"/> - </conditional> - </when> - </conditional> +<tool id="mothur_classify_seqs" name="Classify.seqs" version="1.22.0"> + <description>Assign sequences to taxonomy</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='classify.seqs' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy$:'$taxonomy_out,'^\S+\.tax\.summary$:'$tax_summary + --outputdir='$logfile.extra_files_path' + --fasta=$fasta + --reference=$alignment.template + --taxonomy=$tax.taxonomy + #if $classify.method == 'wang': + --method=$classify.method + #if 15 >= int($classify.ksize.__str__) >= 4: + --ksize=$classify.ksize + #end if + #if int($classify.iters.__str__) > 0: + --iters=$classify.iters + #end if + #if 100 >= int($classify.cutoff.__str__) > 0: + --cutoff=$classify.cutoff + #end if + $classify.probs + #elif $classify.method == 'knn': + --method=$classify.method + --numwanted=$classify.search.numwanted + #if $classify.search.algorithm == 'kmer': + --search=$classify.search.algorithm + --ksize=$classify.search.ksize + #elif $classify.search.algorithm == 'blast': + --search=$classify.search.algorithm + --match=$classify.search.match + --mismatch=$classify.search.mismatch + --gapopen=$classify.search.gapopen + --gapextend=$classify.search.gapextend + #elif $classify.knn.search == 'suffix': + --search=$classify.search.algorithm + #elif $classify.search.algorithm == 'distance': + --search=$classify.search.algorithm + #end if + #end if + --processors=8 + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + $relabund + </command> + <inputs> + <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> + <conditional name="alignment"> + <param name="source" type="select" label="Select Reference Template from" help=""> + <option value="hist">History</option> + <option value="ref">Cached Reference</option> + </param> + <when value="ref"> + <param name="template" type="select" label="reference - Select an alignment database " help=""> + <options from_data_table="mothur_aligndb"> + </options> + </param> + </when> + <when value="hist"> + <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> + </when> + </conditional> + <conditional name="tax"> + <param name="source" type="select" label="Select Taxonomy from" help=""> + <option value="ref">Cached Reference</option> + <option value="hist">History</option> + </param> + <when value="ref"> + <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy reference"> + <options from_data_table="mothur_taxonomy"> + </options> + </param> + </when> + <when value="hist"> + <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy reference"/> + </when> + </conditional> + <conditional name="classify"> + <param name="method" type="select" label="method - Select a classification method" help=""> + <option value="wang">Bayesian (default)</option> + <option value="knn">K-Nearest Neighbor (knn)</option> + </param> + <when value="wang"> + <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"> + <validator type="in_range" message="ksize - kmer length between 5 and 12" min="5" max="12"/> + </param> + <param name="iters" type="integer" value="100" label="iters - iterations to do when calculating the bootstrap confidence score"/> + <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"> + <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/> + </param> + <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/> + </when> + <when value="knn"> + <param name="numwanted" type="integer" value="10" label="numwanted - "/> + <conditional name="search"> + <param name="algorithm" type="select" label="algorithm - " help=""> + <option value="kmer">Kmer (default)</option> + <option value="blast">BLAST</option> + <option value="suffix">Suffix Tree</option> + <option value="distance">Distance</option> + </param> + <when value="kmer"> + <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"/> + </when> + <when value="blast"> + <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> + <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/> + <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> + <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/> + </when> + <when value="suffix"/> + <when value="distance"/> + </conditional> + </when> + </conditional> + + <param name="count" type="data" format="count_table" label="count file" optional="true"/> + + <param name="relabund" type="boolean" falsevalue="" truevalue="--relabund=true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> + + </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -121,7 +127,7 @@ <data format="tax.summary" name="tax_summary" label="${tool.name} on ${on_string}: tax.summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -141,5 +147,7 @@ .. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs +v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang. + </help> </tool>
--- a/mothur/tools/mothur/classify.tree.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/classify.tree.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_classify_tree" name="Classify.tree" version="1.24.0"> +<tool id="mothur_classify_tree" name="Classify.tree" version="1.25.0"> <description>Get a consensus taxonomy for each node on a tree</description> <command interpreter="python"> mothur_wrapper.py @@ -33,7 +33,7 @@ <data format_source="tabular" name="summary" label="${tool.name} on ${on_string}: taxonomy.summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -65,6 +65,7 @@ .. _group: http://www.mothur.org/wiki/Group_file .. _classify.tree: http://www.mothur.org/wiki/Classify.tree +v.1.25.0: Trivial upgrade to Mothur 1.33 </help> </tool>
--- a/mothur/tools/mothur/clearcut.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/clearcut.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_clearcut" name="Clearcut" version="1.19.0"> +<tool id="mothur_clearcut" name="Clearcut" version="1.20.0"> <description>Generate a tree using relaxed neighbor joining</description> <command interpreter="python"> mothur_wrapper.py @@ -64,7 +64,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -90,5 +90,7 @@ .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ .. _clearcut: http://www.mothur.org/wiki/Clearcut +v.1.20.0: Trivial upgrade to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/cluster.classic.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.classic.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.27.0"> +<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.88.0"> <description>Assign sequences to OTUs (Dotur implementation)</description> <command interpreter="python"> mothur_wrapper.py @@ -58,7 +58,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.fragments.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.fragments.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,53 +1,60 @@ -<tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.20.0"> - <description> Group sequences that are part of a larger sequence</description> - <command interpreter="python"> - mothur_wrapper.py - --cmd='cluster.fragments' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fragclust\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names - --outputdir='$logfile.extra_files_path' - --fasta=$fasta - --name=$names - #if int($diffs.__str__) > 0: - --diffs=$diffs - #end if - #if 100 >= int($percent.__str__) > 0: - --percent=$percent - #end if - </command> - <inputs> - <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> - <param name="names" type="data" format="names" optional="true" label="name - Sequences Name reference"/> - <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)"/> - <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" - help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."> - <validator type="in_range" message="percentage differences allowed must be between 0 and 100" min="0" max="100"/> - </param> - </inputs> - <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> - <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> - </outputs> - <requirements> - <requirement type="package" version="1.27">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** +<tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.21.0"> + <description> Group sequences that are part of a larger sequence</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='cluster.fragments' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fragclust\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names + --outputdir='$logfile.extra_files_path' + --fasta=$fasta + --name=$names + #if int($diffs.__str__) > 0: + --diffs=$diffs + #end if + #if 100 >= int($percent.__str__) > 0: + --percent=$percent + #end if +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if + </command> + <inputs> + <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> + <param name="names" type="data" format="names" optional="true" label="name - Sequences Name reference"/> + <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)"/> + <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" + help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."> + <validator type="in_range" message="percentage differences allowed must be between 0 and 100" min="0" max="100"/> + </param> +<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> + <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> + </outputs> + <requirements> + <requirement type="package" version="1.33">mothur</requirement> + </requirements> + <tests> + </tests> + <help> + **Mothur Overview** -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. + Mothur_, initiated by Dr. Patrick Schloss and his software development team + in the Department of Microbiology and Immunology at The University of Michigan, + provides bioinformatics for the microbial ecology community. -.. _Mothur: http://www.mothur.org/wiki/Main_Page + .. _Mothur: http://www.mothur.org/wiki/Main_Page -**Command Documenation** + **Command Documenation** + + The cluster.fragments_ command groups sequences that are part of a larger sequence. -The cluster.fragments_ command groups sequences that are part of a larger sequence. + .. _cluster.fragments: http://www.mothur.org/wiki/Cluster.fragments -.. _cluster.fragments: http://www.mothur.org/wiki/Cluster.fragments + v1.21: Updated to Mothur 1.33. Added count parameter. - </help> + </help> </tool> +
--- a/mothur/tools/mothur/cluster.split.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.split.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_cluster_split" name="Cluster.split" version="1.27.0"> +<tool id="mothur_cluster_split" name="Cluster.split" version="1.28.0"> <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> <command interpreter="python"> mothur_wrapper.py @@ -48,7 +48,8 @@ --precision=$precision #end if $large - --processors=8 + --processors=8 + $cluster </command> <inputs> <conditional name="splitby"> @@ -87,7 +88,9 @@ <param name="taxlevel" type="integer" value="3" label="taxlevel - taxonomy level for split (default=3)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> <param name="classic" type="boolean" checked="false" truevalue="--classic=true" falsevalue="" label="classic - Use cluster.classic" - </when> + /> + +</when> </conditional> <!-- splitby --> <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name="method" type="select" label="method - Select a Clustering Method" help=""> @@ -108,8 +111,11 @@ <option value="100000">.00001</option> <option value="1000000">.000001</option> </param> - <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - distance matrix is too large to fit in RAM" + <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - distance matrix is too large to fit in RAM" help="If your job fails due to not enough memory error, set this to true to rerun"/> + <param name="cluster" type="boolean" falsevalue="" truevalue="--cluster=true" checked="false" label="The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=T. "/> + + </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -121,7 +127,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -140,6 +146,8 @@ .. _cluster.split: http://www.mothur.org/wiki/Cluster.split +v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean. + </help> </tool>
--- a/mothur/tools/mothur/cluster.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cluster.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_cluster" name="Cluster" version="1.27.0"> +<tool id="mothur_cluster" name="Cluster" version="1.28.0"> <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> <command interpreter="python"> mothur_wrapper.py @@ -76,7 +76,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/collect.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/collect.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_collect_shared" name="Collect.shared" version="1.23.0" force_history_refresh="True"> +<tool id="mothur_collect_shared" name="Collect.shared" version="1.24.0" force_history_refresh="True"> <description>Generate collector's curves for calculators on OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -76,8 +76,10 @@ <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option> <option value="structpearson">structpearson - Community Structure Similarity -</option> <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> - <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> + <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> + <option value="Square Root Jensen-Shannon Divergence">Square Root Jensen-Shannon Divergence</option> </param> + <option value="Square Root Jensen-Shannon Divergence">Jensen-Shannon Divergence</option> <param name="freq" type="float" value="0.0" label="freq - "/> <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/> </inputs> @@ -85,7 +87,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/collect.single.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/collect.single.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_collect_single" name="Collect.single" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_collect_single" name="Collect.single" version="1.21.0" force_history_refresh="True"> <description>Generate collector's curves for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -79,7 +79,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/consensus.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/consensus.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.21.0" force_history_refresh="True"> <description>Find a consensus sequence for each OTU or phylotype</description> <command interpreter="python"> mothur_wrapper.py @@ -22,6 +22,9 @@ #else --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta #end if +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if </command> <inputs> <param name="fasta" type="data" format="align" label="fasta - Sequences to Bin" help="Sequences must be the same length"/> @@ -45,6 +48,7 @@ <help>For example: cutoff=95 would return the base that was supported by at least 95% of sequences.</help> <validator type="in_range" message="The percentage cutoff must be between 1 and 100" min="1" max="100"/> </param> +<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -56,7 +60,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cooccurrence.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/cooccurrence.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_cooccurrence" name="Cooccurrence" version="1.25.0" > +<tool id="mothur_cooccurrence" name="Cooccurrence" version="1.26.0" > <description>tests whether presence-absence patterns differ from chance</description> <command interpreter="python"> mothur_wrapper.py @@ -61,7 +61,7 @@ <data format="tabular" name="out_summary" label="${tool.name} on ${on_string}: cooccurence.summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -140,5 +140,7 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _cooccurrence: http://www.mothur.org/wiki/Cooccurrence +v1.26.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/corr.axes.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/corr.axes.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_corr_axes" name="Corr.axes" version="1.20.0"> +<tool id="mothur_corr_axes" name="Corr.axes" version="1.21.0"> <description>correlation of data to axes</description> <command interpreter="python"> mothur_wrapper.py @@ -65,7 +65,7 @@ <data format="axes" name="corr_axes" label="${tool.name} on ${on_string}: corr.axes"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33" >mothur</requirement> </requirements> <tests> </tests> @@ -84,6 +84,8 @@ .. _corr.axes: http://www.mothur.org/wiki/Corr.axes +v.1.21.0: Updated to mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/count.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/count.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,9 +1,9 @@ -<tool id="mothur_count_groups" name="Count.groups" version="1.22.0" > +<tool id="mothur_count_groups" name="Count.groups" version="1.23.0" > <description>counts the number of sequences represented by a specific group or set of groups</description> <command interpreter="python"> mothur_wrapper.py --cmd='count.groups' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups.count$:'$grp_count + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups.count$:'$grp_count,'^\S+\.summary$: '$summary --outputdir='$logfile.extra_files_path' #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$group @@ -47,9 +47,10 @@ <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="grp_count" label="${tool.name} on ${on_string}: group.count" /> + <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/count.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/count.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_count_seqs" name="Count.seqs" version="1.20.0" > +<tool id="mothur_count_seqs" name="Count.seqs" version="1.21.0" > <description>(aka make.table) counts the number of sequences represented by the representative</description> <command interpreter="python"> mothur_wrapper.py @@ -38,7 +38,7 @@ <data format="count_table" name="seq_count" label="${tool.name} on ${on_string}: count_table" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -60,5 +60,7 @@ .. _count.seqs: http://www.mothur.org/wiki/Count.seqs .. _count_table: http://www.mothur.org/wiki/Count_File +v.1.21.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/create.database.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/create.database.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_create_database" name="Create.database" version="1.27.0" > +<tool id="mothur_create_database" name="Create.database" version="1.28.0" > <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description> <command interpreter="python"> mothur_wrapper.py @@ -28,6 +28,7 @@ help="fasta file output by get.oturep"/> <param name="repname" type="data" format="names" label="repname - rep.names" help="names file output by get.oturep"/> + <param name="count" type="data" format="count_table" label="count file - count_table"/> <param name="contaxonomy" type="select" format="cons.taxonomy" label="contaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/> <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/> @@ -42,7 +43,7 @@ <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -63,6 +64,8 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _create.database: http://www.mothur.org/wiki/Create.database +v.1.28.0: Updated to Mothur 1.33, added count paramter. + </help> </tool>
--- a/mothur/tools/mothur/degap.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/degap.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_degap_seqs" name="Degap.seqs" version="1.20.0"> +<tool id="mothur_degap_seqs" name="Degap.seqs" version="1.21.0"> <description>Remove gap characters from sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -15,7 +15,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -34,6 +34,8 @@ .. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs +v1.21.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/deunique.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/deunique.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,23 +1,30 @@ -<tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.20.0"> +<tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.21.0"> <description>Return all sequences</description> <command interpreter="python"> mothur_wrapper.py --cmd='deunique.seqs' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.redundant\.fasta$:'$out_fasta + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.redundant\.fasta$:'$out_fasta,'^\S+\.groups$:'$groups_file --outputdir='$logfile.extra_files_path' - --fasta=$fasta - --name=$names + --fasta=$fasta + #if isinstance($names.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__): + --count=$names + #else + --name=$names + #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> - <param name="names" type="data" format="names" label="names - Sequences Name reference"/> + <param name="names" type="data" format="names,count_table" label="provide a names file OR a count file" help="A names file will generate a new faste file containing all the sequences. If a group file contains group information, a group file will also be created."/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> + <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta"/> + <data format="groups" name="groups_file" label="${tool.name} on ${on_string}: groups"> + <filter>(isinstance($names.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__))</filter> + </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -37,6 +44,8 @@ .. _name: http://www.mothur.org/wiki/Name_file .. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs +v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output + </help> </tool>
--- a/mothur/tools/mothur/deunique.tree.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/deunique.tree.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_deunique_tree" name="Deunique.tree" version="1.20.0"> +<tool id="mothur_deunique_tree" name="Deunique.tree" version="1.21.0"> <description>Reinsert the redundant sequence identiers back into a unique tree.</description> <command interpreter="python"> mothur_wrapper.py @@ -17,7 +17,7 @@ <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: deunique.tre" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -37,6 +37,8 @@ .. _name: http://www.mothur.org/wiki/Name_file .. _deunique.tree: http://www.mothur.org/wiki/Deunique.tree +v1.21.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/dist.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/dist.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_dist_seqs" name="Dist.seqs" version="1.19.0"> +<tool id="mothur_dist_seqs" name="Dist.seqs" version="1.20.0"> <description>calculate uncorrected pairwise distances between aligned sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -49,7 +49,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -70,6 +70,8 @@ .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs +v.1.20.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/dist.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/dist.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_dist_shared" name="Dist.shared" version="1.25.0" force_history_refresh="True"> +<tool id="mothur_dist_shared" name="Dist.shared" version="1.26.0" force_history_refresh="True"> <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> <command interpreter="python"> mothur_wrapper.py @@ -112,13 +112,13 @@ <option value="lt">Phylip formatted Lower Triangle Matrix</option> <option value="square">Phylip formatted Square Matrix</option> </param> - <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each distance matrix"/> + <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each distance matrix"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -139,6 +139,8 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _dist.shared: http://www.mothur.org/wiki/Dist.shared +v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. + </help> </tool>
--- a/mothur/tools/mothur/fastq.info.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/fastq.info.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_fastq_info" name="Fastq.info" version="1.24.0"> +<tool id="mothur_fastq_info" name="Fastq.info" version="1.25.0"> <description>Convert fastq to fasta and quality</description> <command interpreter="python"> mothur_wrapper.py @@ -6,11 +6,74 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile --outputdir='$logfile.extra_files_path' --fastq=$fastq + --pacbio=$pacbio + --format=$format + + #if $oligo.add == "yes": + --oligos=$oligo.oligos + #if $oligo.bdiffs.__str__ != '' and int($oligo.bdiffs.__str__) > 0: + --bdiffs=$oligo.bdiffs + #end if + #if $oligo.pdiffs.__str__ != '' and int($oligo.pdiffs.__str__) > 0: + --pdiffs=$oligo.pdiffs + #end if + #if $oligo.tdiffs.__str__ != '' and int($oligo.tdiffs.__str__) > 0: + --tdiffs=$oligo.tdiffs + #end if + #if $oligo.ldiffs.__str__ != '' and int($oligo.ldiffs.__str__) > 0: + --ldiffs=$oligo.ldiffs + #end if + #if $oligo.sdiffs.__str__ != '' and int($oligo.sdiffs.__str__) > 0: + --sdiffs=$oligo.sdiffs + #end if + --datasetid='$fastq.info.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow' + #end if + </command> <inputs> <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/> <param name="fasta" type="boolean" truevalue="" falsevalue="--fasta=false" checked="true" label="fasta - Add fasta to your history" /> <param name="qfile" type="boolean" truevalue="" falsevalue="--qfile=false" checked="true" label="qfile - Add qfile to your history" /> + + <param name="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false" label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N" /> + <param name="format" type="select" value="sanger" label="format of sequence" > + <option value="sanger">sanger</option> + <option value="solexa">solexa</option> + <option value="illumina">illumina</option> + <option value="illumina1.8+">illumina1.8+</option> + </param> + + <conditional name="oligo"> + <param name="add" type="select" label="Use oligos file?" + help="a file that contain the sequences of the forward and reverse primers and barcodes and their sample identifier. + Each line of the oligos file can start with the key words "forward", "reverse", + and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file. "> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="oligos" type="data" format="oligos" label="oligos - barcodes and primers"/> + <param name="bdiffs" type="integer" value="0" label="bdiffs - number of differences to allow in the barcode (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="pdiffs" type="integer" value="0" label="pdiffs - number of differences to allow in the primer (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="tdiffs" type="integer" value="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="ldiffs" type="integer" value="0" optional="true" label="ldiffs - total number of differences to allow in linker sequence (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="sdiffs" type="integer" value="0" optional="true" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + </when> + </conditional> + + </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -22,7 +85,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/filter.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/filter.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_filter_seqs" name="Filter.seqs" version="1.19.0" force_history_refresh="True"> +<tool id="mothur_filter_seqs" name="Filter.seqs" version="1.20.0" force_history_refresh="True"> <description>removes columns from alignments</description> <command interpreter="python"> mothur_wrapper.py @@ -57,7 +57,7 @@ <data format="align" name="out_fasta" label="${tool.name} on ${on_string}: filtered fasta" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -76,6 +76,8 @@ .. _filter.seqs: http://www.mothur.org/wiki/Filter.seqs +v.1.20.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/get.coremicrobiome.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.coremicrobiome.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="1.26.0"> +<tool id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="1.27.0"> <description>fraction of OTUs for samples or abundances</description> <command interpreter="python"> mothur_wrapper.py @@ -58,7 +58,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -77,6 +77,8 @@ .. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome +v1.27.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/get.group.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.group.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_group" name="Get.group" version="1.19.0"> +<tool id="mothur_get_group" name="Get.group" version="1.20.0"> <description>group names from shared or from list and group</description> <command interpreter="python"> mothur_wrapper.py @@ -15,7 +15,7 @@ <data format="groups" name="bootgroups" label="${tool.name} on ${on_string}: bootGroups" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -34,5 +34,7 @@ .. _get.group: http://www.mothur.org/wiki/Get.group +v.1.20.0: Updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/get.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -8,7 +8,11 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] --cmd='get.groups' --outputdir='$logfile.extra_files_path' - --group=$group_in + #if isinstance($group_in.datatype, $__app__.datatypes_registry.get_datatype_by_extension('groups').__class__): + --group=$group_in + #else + --count=$group_in + #end if #if $groupnames.source == 'groups': #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: --groups=$groupnames.groups @@ -45,7 +49,7 @@ --result=#echo ','.join($results) </command> <inputs> - <param name="group_in" type="data" format="groups" label="group - Groups"/> + <param name="group_in" type="data" format="groups,count_table" label="group or count_table file"/> <conditional name="groupnames"> <param name="source" type="select" label="Select Group Names from"> <option value="groups">A List of Group Names</option> @@ -94,7 +98,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.lineage.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.lineage.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,14 +1,21 @@ -<tool id="mothur_get_lineage" name="Get.lineage" version="1.20.0"> +<tool id="mothur_get_lineage" name="Get.lineage" version="1.21.0"> <description>Picks by taxon</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pick before the last extension to the input file - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] --cmd='get.lineage' + #if $file.filetype.__str__ == "usetaxonomy" + --taxonomy=$file.taxonomy + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] + #else + --constaxonomy=$file.constaxonomy + --shared=$file.shared + --list=$file.list + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy.__str__)) + ":'" + $taxonomy_out.__str__] + #end if --outputdir='$logfile.extra_files_path' - --taxonomy=$taxonomy --taxon="'$re.sub('(\s|,)+',',',$re.sub('\(\d+\)','',$taxon.value.__str__))'" #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: --fasta=$fasta_in @@ -30,11 +37,28 @@ --name=$name_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] $dups - #end if + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if --result=#echo ','.join($results) </command> <inputs> - <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> + <conditional name ="file"> + <param name = "filetype" type = "select" label="choose which file is used"> + <option value = "usetaxonomy" selected = "true">taxonomy</option> + <option value = "useconstaxonomy">constaxonomy</option> + </param> + <when value = "usetaxonomy"> + <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> + </when> + <when value = "useconstaxonomy"> + <param name="constaxonomy" type="data" format="cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file"/> + <param name="shared" type="data" format="shared" label="shared - shared file" optional="true"/> + <param name="list" type="data" format="list" label="list - list file" optional="true"/> + </when> + </conditional> + <!-- <param name="taxons" type="select" size="120" multiple="true" label="Browse Taxons from Taxonomy"> <options from_dataset="taxonomy"> @@ -51,7 +75,8 @@ <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/> <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> - <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/> + <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/> + <param name = "count" type="data" format="count_table" optional="true" help ="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -73,7 +98,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.otulabels.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.otulabels.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_otulabels" name="Get.otulabels" version="1.26.0"> +<tool id="mothur_get_otulabels" name="Get.otulabels" version="1.27.0"> <description>Selects OTU labels</description> <command interpreter="python"> mothur_wrapper.py @@ -20,13 +20,21 @@ --corraxes=$corraxes_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($corraxes_in.__str__)) + ":'" + $corraxes_out.__str__] #end if - --result=#echo ','.join($results) + --result=#echo ','.join($results) + #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: + --list=$list + #end if + #if $shared_in.__str__ != "None" and len($shared_in.__str__) > 0: + --shared=$shared + #end if </command> <inputs> <param name="accnos" type="data" format="otulabels" label="accnos - otulabels" help="At least one of constaxonomy, otucorr, or corraxes must be given"/> <param name="constaxonomy_in" type="data" format="cons.taxonomy" optional="true" label="constaxonomy - Consensus Taxonomy from classify.otu"/> <param name="otucorr_in" type="data" format="otu.corr" optional="true" label="otucorr - OTU correlation from otu.association"/> <param name="corraxes_in" type="data" format="axes" optional="true" label="corraxes - axes from corr.axes"/> + <param name="list" type="data" format="list" optional="true" label="list - allows you to input a list file you wish to select OTUs from. "/> + <param name="shared" type="data" format="shared" optional="true" label="shared - allows you to input a shared file you wish to select OTUs from. "/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -43,7 +51,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -65,5 +73,7 @@ .. _otu.association: http://www.mothur.org/wiki/Otu.association .. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels +v.1.27.0: Aded list and shared parameters, updated to Mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/get.otulist.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.otulist.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_otulist" name="Get.otulist" force_history_refresh="True" version="1.19.0"> +<tool id="mothur_get_otulist" name="Get.otulist" force_history_refresh="True" version="1.20.0"> <description>Get otus for each distance in a otu list</description> <command interpreter="python"> mothur_wrapper.py @@ -38,7 +38,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -57,6 +57,7 @@ .. _get.otulist: http://www.mothur.org/wiki/Get.otulist +v.1.20.0: Updated to Mothur 1.33 </help> </tool>
--- a/mothur/tools/mothur/get.oturep.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.oturep.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_oturep" name="Get.oturep" version="1.23.0" force_history_refresh="True"> +<tool id="mothur_get_oturep" name="Get.oturep" version="1.23.0" force_history_refresh="true"> <description>Generate a fasta with a representative sequence for each OTU</description> <command interpreter="python"> mothur_wrapper.py @@ -36,7 +36,13 @@ #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: --sorted=$sorted #end if + #if $method.__str__ != "None" and len($method.__str__) > 0: + --method=$method + #end if $large + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <!-- get.relabund relabund type should also work --> @@ -85,12 +91,17 @@ </param> <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name ="method" type="select" label="method - select the method of selecting the representative sequence" help="the distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the abundant sequence in the OTU as the representative" optional = "true"> + <option value="distance">distance</option> + <option value="abundance">abundance</option> + </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -109,5 +120,7 @@ .. _get.oturep: http://www.mothur.org/wiki/Get.oturep +v1.23.0: Updated to Mothur 1.33, added count and method parameter + </help> </tool>
--- a/mothur/tools/mothur/get.otus.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.otus.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_otus" name="Get.otus" version="1.19.0"> +<tool id="mothur_get_otus" name="Get.otus" version="1.20.0"> <description>Get otus containing sequences from specified groups</description> <command interpreter="python"> mothur_wrapper.py @@ -55,7 +55,7 @@ <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -75,6 +75,7 @@ .. _list: http://www.mothur.org/wiki/List_file .. _get.otus: http://www.mothur.org/wiki/Get.otus +v.1.20.0: Updated to Mothur 1.33 </help> </tool>
--- a/mothur/tools/mothur/get.rabund.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.rabund.xml Fri Oct 31 15:09:32 2014 -0400 @@ -14,6 +14,9 @@ --label=$label #end if $sorted + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <param name="otu" type="data" format="list,sabund" label="list,sabund - List or Sabund"/> @@ -24,13 +27,14 @@ </param> <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - sort by abundance" help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.relabund.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.relabund.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_relabund" name="Get.relabund" version="1.20.0"> +<tool id="mothur_get_relabund" name="Get.relabund" version="1.21.0"> <description>Calculate the relative abundance of each otu</description> <command interpreter="python"> mothur_wrapper.py @@ -42,7 +42,7 @@ <data format="relabund" name="relabund" label="${tool.name} on ${on_string}: relabund" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -62,5 +62,6 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _get.relabund: http://www.mothur.org/wiki/Get.relabund +v.1.21.0: Updated to Mothur 1.33 </help> </tool>
--- a/mothur/tools/mothur/get.sabund.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.sabund.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,54 +1,59 @@ -<tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0"> - <description>Get sabund from a otu list or rabund</description> - <command interpreter="python"> - mothur_wrapper.py - --cmd='get.sabund' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund - --outputdir='$logfile.extra_files_path' - #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): - --list=$otu - #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): - --rabund=$otu - #end if - #if $label.__str__ != "None" and len($label.__str__) > 0: - --label=$label - #end if - </command> - <inputs> - <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/> - <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> - <options> - <filter type="data_meta" ref="otu" key="labels" /> - </options> - </param> - </inputs> - <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> - </outputs> - <requirements> - <requirement type="package" version="1.27">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** +<tool id="mothur_get_sabund" name="Get.sabund" version="1.20.0"> + <description>Get sabund from a otu list or rabund</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='get.sabund' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund + --outputdir='$logfile.extra_files_path' + #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): + --list=$otu + #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): + --rabund=$otu + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label=$label + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + </command> + <inputs> + <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/> + <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> + <options> + <filter type="data_meta" ref="otu" key="labels" /> + </options> + </param> + <param name = "count" type="data" format="count_table" optional="true" help ="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/> -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. - -.. _Mothur: http://www.mothur.org/wiki/Main_Page + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> + </outputs> + <requirements> + <requirement type="package" version="1.33">mothur</requirement> + </requirements> + <tests> + </tests> + <help> + **Mothur Overview** -**Command Documenation** + Mothur_, initiated by Dr. Patrick Schloss and his software development team + in the Department of Microbiology and Immunology at The University of Michigan, + provides bioinformatics for the microbial ecology community. -The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file. + .. _Mothur: http://www.mothur.org/wiki/Main_Page -.. _sabund: http://www.mothur.org/wiki/Sabund_file -.. _list: http://www.mothur.org/wiki/List_file -.. _rabund: http://www.mothur.org/wiki/Rabund_file -.. _get.sabund: http://www.mothur.org/wiki/Get.sabund + **Command Documenation** + + The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file. + + .. _sabund: http://www.mothur.org/wiki/Sabund_file + .. _list: http://www.mothur.org/wiki/List_file + .. _rabund: http://www.mothur.org/wiki/Rabund_file + .. _get.sabund: http://www.mothur.org/wiki/Get.sabund - </help> + </help> </tool>
--- a/mothur/tools/mothur/get.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -38,6 +38,12 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] #end if --result=#echo ','.join($results) + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + #if $fastq.__str__ != "None" and len($fastq.__str__) > 0: + --fastq=$fastq + #end if </command> <inputs> <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/> @@ -49,6 +55,8 @@ <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name="fastq" type="data" format="fastq" optional="true" label="count - a count_table" help="fastq - allows you to select sequences from your fastq file"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -77,7 +85,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -102,5 +110,7 @@ .. _list.seqs: http://www.mothur.org/wiki/list.seqs .. _get.seqs: http://www.mothur.org/wiki/Get.seqs +v.1.27.0 : Updated to Mothur 1.33, added count and fastq params + </help> </tool>
--- a/mothur/tools/mothur/get.sharedseqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/get.sharedseqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_sharedseqs" name="Get.sharedseqs" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_get_sharedseqs" name="Get.sharedseqs" version="1.21.0" force_history_refresh="True"> <description>Get shared sequences at each distance from list and group</description> <command interpreter="python"> mothur_wrapper.py @@ -6,8 +6,12 @@ --cmd='get.sharedseqs' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' - --list=$list - --group=$group + #if isinstance($list.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): + --list=$list + --group=$group + #else + --shared=$list + #end if #set datasets = ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.seqs)$:tabular'"] #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' @@ -35,8 +39,8 @@ #end if </command> <inputs> - <param name="list" type="data" format="list" label="list - OTU List"/> - <param name="group" type="data" format="groups" label="group - "/> + <param name="list" type="data" format="list,shared" label="list - OTU List or shared file"/> + <param name="group" type="data" format="groups" label="group - not required if using a shared file"/> <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> <options> @@ -78,7 +82,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -97,5 +101,7 @@ .. _get.sharedseqs: http://www.mothur.org/wiki/Get.sharedseqs +v1.21.0: Updated to Mothur 1.33, added shared file option + </help> </tool>
--- a/mothur/tools/mothur/hcluster.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/hcluster.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_hcluster" name="Hcluster" version="1.19.0"> +<tool id="mothur_hcluster" name="Hcluster" version="1.20.0"> <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> <command interpreter="python"> mothur_wrapper.py @@ -76,7 +76,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/heatmap.bin.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/heatmap.bin.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.21.0" force_history_refresh="True"> <description>Generate a heatmap for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -102,7 +102,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -123,5 +123,6 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin +v.1.21.0: Updated to Mothur 1.33 </help> </tool>
--- a/mothur/tools/mothur/heatmap.sim.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/heatmap.sim.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.23.0" force_history_refresh="True"> +<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.24.0" force_history_refresh="True"> <description>Generate a heatmap for pariwise similarity</description> <command interpreter="python"> mothur_wrapper.py @@ -35,6 +35,9 @@ #if 100 > $fontsize > 0: --fontsize=$fontsize #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <conditional name="input"> @@ -78,6 +81,7 @@ </conditional> <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -86,7 +90,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -109,5 +113,6 @@ .. _name: http://www.mothur.org/wiki/Name_file .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim +v.1.24.0: Updated to Mothur 1.33, added count parameter </help> </tool>
--- a/mothur/tools/mothur/homova.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/homova.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_homova" name="Homova" version="1.19.0"> +<tool id="mothur_homova" name="Homova" version="1.20.0"> <description>Homogeneity of molecular variance</description> <command interpreter="python"> mothur_wrapper.py @@ -13,20 +13,28 @@ #if float($alpha.__str__) > 0.0: --alpha=$alpha #end if + #if $sets.__str__ != "None" and len ($sets.__str__) >0: + --sets=$sets + #end if </command> <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> - <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> + <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> +<param name="sets" type="select" label="sets - Which of the sets in your design file you would like to analyze. The set names are separated by dashes. The defualt is all sets in designfile" multiple = "true"> + <options> + <filter type="data_meta" ref="design" key="sets"/> + </options> + </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="homova" label="${tool.name} on ${on_string}: homova"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -57,6 +65,7 @@ .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _homova: http://www.mothur.org/wiki/Homova +v.1.20.0: Updated to Mothur 1.33, added sets parameter </help> </tool>
--- a/mothur/tools/mothur/indicator.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/indicator.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_indicator" name="Indicator" version="1.21.0"> +<tool id="mothur_indicator" name="Indicator" version="1.22.0"> <description>Identify indicator "species" for nodes on a tree</description> <command interpreter="python"> mothur_wrapper.py @@ -51,7 +51,7 @@ <data format="tabular" name="summary" label="${tool.name} on ${on_string}: indicator.summary"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -72,6 +72,7 @@ .. _relabund: http://www.mothur.org/wiki/Get.relabund .. _indicator: http://www.mothur.org/wiki/Indicator +v.1.22.0: Updated to Mothur 1.33 </help> </tool>
--- a/mothur/tools/mothur/libshuff.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/libshuff.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_libshuff" name="Libshuff" version="1.19.0"> +<tool id="mothur_libshuff" name="Libshuff" version="1.20.0"> <description>Cramer-von Mises tests communities for the same structure</description> <command interpreter="python"> mothur_wrapper.py @@ -52,7 +52,7 @@ <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/list.otulabels.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/list.otulabels.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_list_otulabels" name="List.otulabels" version="1.26.0"> +<tool id="mothur_list_otulabels" name="List.otulabels" version="1.27.0"> <description>Lists otu labels from shared or relabund file</description> <command interpreter="python"> mothur_wrapper.py @@ -8,7 +8,9 @@ #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$otu #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): - --relabund=$otu + --relabund=$otu + #else + --list=$otu #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label=$label @@ -18,7 +20,7 @@ #end if </command> <inputs> - <param name="otu" type="data" format="shared,relabund" label="shared or relabund - OTU Shared or Relabund"/> + <param name="otu" type="data" format="shared,relabund,list" label="shared or relabund - OTU Shared or Relabund"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options> <filter type="data_meta" ref="otu" key="labels" /> @@ -35,7 +37,7 @@ <data format="otulabels" name="otulabels" label="${tool.name} on ${on_string}: otulabels"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -61,6 +63,7 @@ .. _shared: http://www.mothur.org/wiki/Shared_file .. _relabund: http://www.mothur.org/wiki/Get.relabund +v.1.27.0: Updated to mothur 1.33, added list file for otu </help> </tool>
--- a/mothur/tools/mothur/list.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/list.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_list_seqs" name="List.seqs" version="1.19.0"> +<tool id="mothur_list_seqs" name="List.seqs" version="1.20.0"> <description>Lists the names (accnos) of the sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -18,6 +18,9 @@ #elif $search.type == "taxonomy": --taxonomy=$search.input #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <conditional name="search"> @@ -48,6 +51,8 @@ <param name="input" type="data" format="seq.taxonomy" label="taxonomy - Sequence Taxonomy"/> </when> </conditional> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name="count" type="data" format="fastq" optional="true" label="fastq"/> </inputs> <outputs> <!-- fix format --> @@ -55,7 +60,7 @@ <data format="accnos" name="out_file" label="${tool.name} on ${on_string}: accnos" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -79,6 +84,7 @@ .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _list.seqs: http://www.mothur.org/wiki/list.seqs +v.1.20.0: Updated to mothur 1.33, added count and fastq option </help> </tool>
--- a/mothur/tools/mothur/make.biom.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.biom.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,72 +1,95 @@ -<tool id="mothur_make_biom" name="Make.biom" version="1.25.0" force_history_refresh="True"> - <description>Make biom files from a shared file</description> - <command interpreter="python"> - mothur_wrapper.py - #import re, os.path - --cmd='make.biom' - --result='^mothur.\S+\.logfile$:'$logfile - --outputdir='$logfile.extra_files_path' - --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.((\S+)\.biom)$:biom' - --shared=$shared - #if $contaxonomy != 'none' and len($contaxonomy.__str__) > 0: - --contaxonomy=$contaxonomy - #end if - #if $label.__str__ != "None" and len($label.__str__) > 0: - --label='$label' - #end if - #if $groups.__str__ != "None" and len($groups.__str__) > 0: - --groups=$groups - #end if - --matrixtype=$matrixtype - </command> - <inputs> - <param name="shared" type="data" format="shared" label="shared - OTU Shared file"/> - <param name="contaxonomy" type="data" format="cons.taxonomy" label="contaxonomy - consensus taxonomy" - help="The contaxonomy file is the taxonomy file outputted by classify.otu"/> - <param name="matrixtype" type="select" label="matrixtype - sparse or dense"> - <option value="sparse">sparse</option> - <option value="dense">dense</option> - </param> - <param name="groups" type="select" label="groups - Groups to include" multiple="true" - help="By default all are included if no selection is made."> - <options> - <filter type="data_meta" ref="shared" key="groups" /> - </options> - </param> - <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" - help="By default all are included if no selection is made."> - <options> - <filter type="data_meta" ref="shared" key="labels" /> - </options> - </param> - </inputs> - <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - </outputs> - <requirements> - <requirement type="package" version="1.27">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** +<tool id="mothur_make_biom" name="Make.biom" version="1.26.0" force_history_refresh="True"> + <description>Make biom files from a shared file</description> + <command interpreter="python"> + mothur_wrapper.py + #import re, os.path + --cmd='make.biom' + --result='^mothur.\S+\.logfile$:'$logfile + --outputdir='$logfile.extra_files_path' + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.((\S+)\.biom)$:biom' + --shared=$shared + #if $contaxonomy.__str__ != 'None' and len($contaxonomy.__str__) > 0: + --constaxonomy=$contaxonomy + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label='$label' + #end if + #if $groups.__str__ != "None" and len($groups.__str__) > 0: + --groups=$groups + #end if + --matrixtype=$matrixtype + #if $metadata.__str__ != 'None' and len($metadata.__str__) > 0: + --metadata=$metadata + #end if + #if $picrustc.use: + #if $picrustc.picrust.__str__ != '': + --picrust=$picrustc.picrust + #end if + #if $picrustc.reftax.__str__ != '': + --reftaxonomy=$picrustc.reftax + #end if + #end if + </command> + <inputs> + <param name="shared" type="data" format="shared" label="shared - OTU Shared file"/> + <param name="contaxonomy" type="data" format="cons.taxonomy" label="contaxonomy - consensus taxonomy" + help="The contaxonomy file is the taxonomy file outputted by classify.otu" + optional="true" + /> + <param name = "metadata" type = "data" format = "metadata" label = "metadata" optional="true" help="You can add sample data support here."/> + <conditional name = "picrustc"> + <param name = "use" type = "boolean" truevalue = "yes" falsevalue = "no" checked="false" label = "use picrust program"/> + <when value = "yes"> + <param name = "picrust" type = "data" format ="otu_map" label = "picrust" help="The picrust program requires green genes OTU IDs. The picrust parameter allows you to provide the OTU ID mapping table associated with your reference taxonomy."/> + <param name = "reftax" type = "data" format = "tax" label = "reftaxonomy" help="The referencetax parameter is used with the picrust parameter. Picrust requires the greengenes OTU IDs to be in the biom file, and the referencetax parameter allows you to provide your reference taxonomy file you used when classifying your sequences."/> + </when> + <when value = "no"/> + </conditional> -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. + <param name="matrixtype" type="select" label="matrixtype - sparse or dense"> + <option value="sparse">sparse</option> + <option value="dense">dense</option> + </param> + <param name="groups" type="select" label="groups - Groups to include" multiple="true" + help="By default all are included if no selection is made."> + <options> + <filter type="data_meta" ref="shared" key="groups" /> + </options> + </param> + <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" + help="By default all are included if no selection is made."> + <options> + <filter type="data_meta" ref="shared" key="labels" /> + </options> + </param> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + </outputs> + <requirements> + <requirement type="package" version="1.33">mothur</requirement> + </requirements> + <tests> + </tests> + <help> + **Mothur Overview** -.. _Mothur: http://www.mothur.org/wiki/Main_Page + Mothur_, initiated by Dr. Patrick Schloss and his software development team + in the Department of Microbiology and Immunology at The University of Michigan, + provides bioinformatics for the microbial ecology community. -**Command Documenation** + .. _Mothur: http://www.mothur.org/wiki/Main_Page -The make.biom command converts a shared_ shared file to biom_ files. -The output can be filtered by groups and labels. + **Command Documenation** + + The make.biom command converts a shared_ shared file to biom_ files. + The output can be filtered by groups and labels. -.. _shared: http://www.mothur.org/wiki/Shared_file -.. _biom: http://biom-format.org/documentation/biom_format.html -.. _make.biom: http://www.mothur.org/wiki/Make.biom + .. _shared: http://www.mothur.org/wiki/Shared_file + .. _biom: http://biom-format.org/documentation/biom_format.html + .. _make.biom: http://www.mothur.org/wiki/Make.biom - </help> + </help> </tool>
--- a/mothur/tools/mothur/make.contigs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.contigs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_make_contigs" name="Make.contigs" version="1.26.0"> +<tool id="mothur_make_contigs" name="Make.contigs" version="1.27.0"> <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description> <command interpreter="python"> mothur_wrapper.py @@ -19,6 +19,12 @@ #if $oligo.tdiffs.__str__ != '' and int($oligo.tdiffs.__str__) > 0: --tdiffs=$oligo.tdiffs #end if + #if $oligo.findex.__str__ != 'None': + --findex=$oligo.findex + #end if + #if $oligo.rindex.__str__ != 'None': + --rindex=$oligo.rindex + #end if #end if #if $match.__str__ != '': @@ -65,6 +71,8 @@ <param name="tdiffs" type="integer" value="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"> <validator type="in_range" message="Number of differences can't be negative" min="0"/> </param> + <param name="findex" type = "data" format="fastq" optional="true" label="forward index file (fastq)"/> + <param name="rindex" type = "data" format="fastq" optional="true" label="revese index file (fastq)"/> </when> </conditional> <param name="match" type="integer" value="1" optional="true" label="match - Pairwise alignment reward for a match"/> @@ -85,7 +93,7 @@ <data format="txt" name="cmismatch" label="${tool.name} on ${on_string}: contigs.mismatch"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -104,5 +112,7 @@ .. _make.contigs: http://www.mothur.org/wiki/Make.contigs +v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file. + </help> </tool>
--- a/mothur/tools/mothur/make.design.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.design.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_make_design" name="Make Design" version="1.19.0" > +<tool id="mothur_make_design" name="Make Design" version="1.20.0" > <description>Assign groups to Sets</description> <command> cat $generated_design > $design </command> @@ -29,7 +29,7 @@ <data format="design" name="design" label="${tool.name} on ${on_string}: design" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.fastq.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.fastq.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,48 +1,65 @@ -<tool id="mothur_make_fastq" name="Make.fastq" version="1.19.0"> - <description>Convert fasta and quality to fastq</description> - <command interpreter="python"> - mothur_wrapper.py - --cmd='make.fastq' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq - --outputdir='$logfile.extra_files_path' - --fasta=$fasta - --qfile=$qfile - </command> - <inputs> - <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> - <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> - </inputs> - <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq"> - <change_format> - <when input="qfile.ext" value="qual454" format="fastqsanger"/> - <when input="qfile.ext" value="qualillumina" format="fastqillumina"/> - <when input="qfile.ext" value="qualsolexa" format="fastqsolexa"/> - <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/> - </change_format> - </data> - </outputs> - <requirements> - <requirement type="package" version="1.27">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** +<tool id="mothur_make_fastq" name="Make.fastq" version="1.20.0"> + <description>Convert fasta and quality to fastq</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='make.fastq' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq + --outputdir='$logfile.extra_files_path' + --fasta=$fasta + --qfile=$qfile + #if $chooseformat.use: + --format=$chooseformat.format + #end if + </command> + <inputs> + <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> + <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> + + <conditional name = "chooseformat"> + <param name = "use" type ="boolean" truevalue ="yes" falsevalue="no" label="choose what format your sequences are"/> -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. + <when value = "yes"> + <param name = "format" type = "select" optional = "true" multiple = "true"> + <option value = "sanger" selected="true">sanger</option> + <option value = "solexa">solexa</option> + <option value = "illumina">illumina</option> + <option value = "illumina">illumina1.8+</option> + </param> + </when> + <when value = "no"/> + </conditional> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq"> + <change_format> + <when input="qfile.ext" value="qual454" format="fastqsanger"/> + <when input="qfile.ext" value="qualillumina" format="fastqillumina"/> + <when input="qfile.ext" value="qualsolexa" format="fastqsolexa"/> + <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="package" version="1.33">mothur</requirement> + </requirements> + <tests> + </tests> + <help> + **Mothur Overview** -.. _Mothur: http://www.mothur.org/wiki/Main_Page + Mothur_, initiated by Dr. Patrick Schloss and his software development team + in the Department of Microbiology and Immunology at The University of Michigan, + provides bioinformatics for the microbial ecology community. -**Command Documenation** + .. _Mothur: http://www.mothur.org/wiki/Main_Page -The fastq.info_ command reads a fasta file and quality file and creates a fastq. + **Command Documenation** + + The fastq.info_ command reads a fasta file and quality file and creates a fastq. -.. _fastq.info: http://www.mothur.org/wiki/Make.fastq + .. _fastq.info: http://www.mothur.org/wiki/Make.fastq - </help> + </help> </tool>
--- a/mothur/tools/mothur/make.group.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.group.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_make_files" name="Make.group" version="1.19.0"> +<tool id="mothur_make_files" name="Make.group" version="1.20.0"> <description>Make a group file</description> <command interpreter="python"> mothur_wrapper.py @@ -21,7 +21,7 @@ <data format="groups" name="output" label="${tool.name} on ${on_string}: group" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/make.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_make_shared" name="Make.shared" version="1.22.0" force_history_refresh="True"> +<tool id="mothur_make_shared" name="Make.shared" version="1.23.0" force_history_refresh="True"> <description>Make a shared file from a list and a group</description> <command interpreter="python"> mothur_wrapper.py @@ -10,8 +10,14 @@ --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' #end if - --list=$list - --group=$group + --list=$list + + #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('groups').__class__): + --group=$group + #else: + --count=$group + #end if + #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if @@ -26,7 +32,7 @@ </command> <inputs> <param name="list" type="data" format="list" label="list - OTU List"/> - <param name="group" type="data" format="groups" label="group - "/> + <param name="group" type="data" format="groups, count" label="group - "/> <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> <options> @@ -48,7 +54,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/mantel.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/mantel.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_mantel" name="Mantel" version="1.19.0"> +<tool id="mothur_mantel" name="Mantel" version="1.20.0"> <description>Mantel correlation coefficient between two matrices.</description> <command interpreter="python"> mothur_wrapper.py @@ -27,7 +27,7 @@ <data format="tabular" name="mantel" label="${tool.name} on ${on_string}: mantel"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/merge.files.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/merge.files.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_merge_files" name="Merge.files" version="1.19.0"> +<tool id="mothur_merge_files" name="Merge.files" version="1.20.0"> <description>Merge data</description> <command interpreter="python"> mothur_wrapper.py @@ -54,7 +54,7 @@ <data format="input" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/merge.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/merge.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_merge_groups" name="Merge.groups" version="1.24.0" > +<tool id="mothur_merge_groups" name="Merge.groups" version="1.25.0" > <description>Merge groups in a shared file</description> <command interpreter="python"> mothur_wrapper.py @@ -85,7 +85,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/merge.sfffiles.xml Fri Oct 31 15:09:32 2014 -0400 @@ -0,0 +1,45 @@ +<tool id="mothur_merge_sfffiles" name="Merge.sfffiles" version="1.1.0"> + <description>Merge SFF files</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='merge.sfffiles' + --result='^mothur.\S+\.logfile$:'$logfile,'mergefile:'$output + --outputdir='$logfile.extra_files_path' + --sff=${input}#for i in $inputs#,${i.input}#end for# + --output='mergefile' + </command> + <inputs> + + <param name="input" type="data" format="sff" label="input - sff"/> + <repeat name="inputs" title="Addition SFF files to merge"> + <param name="input" type="data" format="sff" label="input - sff"/> + </repeat> + + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="input" name="output" label="${tool.name} on ${on_string}: merged sff"/> + </outputs> + <requirements> + <requirement type="package" version="1.33">mothur</requirement> + </requirements> + <tests> + </tests> + <help> +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The merge.sfffiles_ command merge inputs into a single output. + +.. _merge.sfffiles: http://www.mothur.org/wiki/Merge.sfffiles + + + </help> +</tool>
--- a/mothur/tools/mothur/metastats.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/metastats.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_metastats" name="Metastats" version="1.20.0" force_history_refresh="True" > +<tool id="mothur_metastats" name="Metastats" version="1.21.0" force_history_refresh="True" > <description>generate principle components plot data</description> <command interpreter="python"> mothur_wrapper.py @@ -55,7 +55,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -74,5 +74,7 @@ .. _metastats: http://www.mothur.org/wiki/Metastats +v.1.21.0: Updated to mothur 1.33 + </help> </tool>
--- a/mothur/tools/mothur/mothur_wrapper.py Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/mothur_wrapper.py Fri Oct 31 15:09:32 2014 -0400 @@ -44,8 +44,8 @@ assert sys.version_info[:2] >= ( 2, 4 ) -debug = False -#debug = True +#debug = False +debug = True max_processors = os.getenv('MOTHUR_MAX_PROCESSORS') if os.getenv('MOTHUR_MAX_PROCESSORS') else 8 def stop_err( msg ): @@ -53,6 +53,7 @@ sys.exit() def __main__(): + global debug # tranform the logfile into html # add extra file ouput # add object tags for svg files @@ -67,15 +68,15 @@ html.write("<html><head><title>%s</title></head>\n<body>\n<pre>\n" % title) try: for line in txt: - if line.find('set.dir') >= 0: + if line.find('set.dir') >= 0: continue - elif line.find('put directory to ') >= 0: + elif line.find('put directory to ') >= 0: continue - elif line.startswith('Mothur\'s directories:') : + elif line.startswith('Mothur\'s directories:') : continue - elif line.startswith('outputDir=') : + elif line.startswith('outputDir=') : continue - elif line.startswith('Type ') : + elif line.startswith('Type ') : continue elif line.find(tmp_output_dir_name) >= 0: # if debug: print >> sys.stdout, 'logfile_to_html #%s#' % line @@ -119,7 +120,7 @@ except: shutil.copy(val,os.path.join(input_dir,fname)) vals.append(fname) - if debug: print >> sys.stderr, "scp %s %s" % (val, os.path.join(input_dir,fname)) + if debug: print >> sys.stdout, "scp %s %s" % (val, os.path.join(input_dir,fname)) else: vals.append(convert_value(val)) return '-'.join(vals) @@ -164,10 +165,10 @@ Gather parameter values for the specified mothur command 'cmd', using the definition from the 'cmd_dict' dictionary. """ - if debug: print >> sys.stderr, options + if debug: print >> sys.stdout, options params = [] for opt in cmd_dict[cmd]['required']: - if debug: print >> sys.stderr, opt + if debug: print >> sys.stdout, opt if isinstance(opt,list): # One of these must be present missing = True for sel in opt: @@ -212,33 +213,33 @@ The complexity of inputs should be handled by the glaxy tool xml file. """ cmd_dict = dict() - cmd_dict['align.check'] = dict({'required' : ['fasta','map']}) + cmd_dict['align.check'] = dict({'required' : ['fasta','map'], 'optional' : ['name','count']}) cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','save','processors']}) - cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) + cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters','sets']}) cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) - cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']}) + cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group','count']}) cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']}) #catchall cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']}) cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','save','processors']}) cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','save','processors']}) - cmd_dict['chimera.perseus'] = dict({'required' : ['fasta','name'], 'optional' : ['group','alpha','beta','cutoff']}) + cmd_dict['chimera.perseus'] = dict({'required' : ['fasta',['name','count']], 'optional' : ['group','alpha','beta','cutoff','dereplicate']}) cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','save','processors']}) - cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','group','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors']}) - cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','group','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']}) - cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']}) - cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) - cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','save','processors']}) + cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','group','count','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors','dereplicate']}) + cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','group','count','dereplicate','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']}) + cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short','name','group','count']}) + cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy','count','persample']}) + cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','save','processors','count','relabund']}) cmd_dict['classify.tree'] = dict({'required' : ['taxonomy','tree'],'optional' : ['name','group','cutoff']}) #clear.memory ## not needed in galaxy framework cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']}) cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','count','method','cutoff','hard','precision','sim','showabund','timing']}) cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','count','method','cutoff','hard','sim','precision']}) - cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']}) - cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','count','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','classic','timing','processors']}) + cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent','count']}) + cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','count','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','classic','timing','processors','cluster']}) cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']}) cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']}) - cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']}) + cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff','count']}) cmd_dict['cooccurrence'] = dict({'required' : ['shared'], 'optional' : ['iters','metric','matrixmodel','groups','label']}) @@ -246,40 +247,40 @@ cmd_dict['count.groups'] = dict({'required' : [['group','shared','count']], 'optional' : ['accnos','groups']}) cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups','large']}) - cmd_dict['create.database'] = dict({'required' : [['list','shared'],'repfasta','repname','contaxonomy'], 'optional' : ['group','label']}) + cmd_dict['create.database'] = dict({'required' : [['list','shared'],'repfasta','repname','constaxonomy','count'], 'optional' : ['group','label']}) cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) - cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) + cmd_dict['deunique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','count']}) cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'], 'optional' : []}) cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']}) cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','subsample','iters','processors']}) - cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : ['fasta','qfile']}) + cmd_dict['fastq.info'] = dict({'required' : ['fastq','format'], 'optional' : ['fasta','qfile','pacbio','oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs']}) cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []}) cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design']}) cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']}) - cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted']}) + cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted','count','method']}) cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) - cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']}) + cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label','count']}) cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']}) - cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']}) - cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) - cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']}) + cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label','count']}) + cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups','count','fastq']}) + cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta','shared']}) cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']}) cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) - cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize']}) - cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) + cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize','count']}) + cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters','sets']}) cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']}) cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']}) cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) - - cmd_dict['make.biom'] = dict({'required' : ['shared'] , 'optional' : ['contaxonomy','matrixtype','groups','label']}) - cmd_dict['make.contigs'] = dict({'required' : ['ffastq','rfastq',], 'optional' : ['align','match','mismatch','gapopen','gapextend','threshold','oligos','bdiffs','pdiffs','tdiffs','processors']}) + cmd_dict['list.otulabels'] = dict({'required': [['shared','relabund','list']], 'optional': ['group','label']}) + cmd_dict['make.biom'] = dict({'required' : ['shared'] , 'optional' : ['constaxonomy','matrixtype','groups','label','metadata','picrust','reftaxonomy']}) + cmd_dict['make.contigs'] = dict({'required' : ['ffastq','rfastq',], 'optional' : ['align','match','mismatch','gapopen','gapextend','threshold','oligos','bdiffs','pdiffs','tdiffs','processors','rindex','findex']}) - cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) + cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : ['format']}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) - cmd_dict['make.shared'] = dict({'required' : [['list','group','biom']], 'optional' : ['label','groups']}) + cmd_dict['make.shared'] = dict({'required' : [['list','group','biom','count']], 'optional' : ['label','groups']}) cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']}) cmd_dict['merge.files'] = dict({'required' : ['input','output']}) cmd_dict['merge.groups'] = dict({'required' : [['shared','group'],'design'], 'optional' : ['groups', 'label']}) @@ -289,46 +290,48 @@ cmd_dict['otu.association'] = dict({'required' : [['shared','relabund']], 'optional' : ['groups', 'label','method','metadata']}) cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']}) cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) - cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) - cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']}) + cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label','count']}) + cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors','count']}) cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']}) cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']}) - cmd_dict['pcr.seqs'] = dict({'required' : ['fasta'], 'optional' : ['oligos','name','group','taxonomy','ecoli','start','end','nomatch','keepprimer','keepdots','processors']}) + cmd_dict['pcr.seqs'] = dict({'required' : ['fasta'], 'optional' : ['oligos','name','group','taxonomy','ecoli','start','end','nomatch','keepprimer','keepdots','processors','count','pdiffs']}) - cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']}) + cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors','count']}) cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) - cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs','group','processors']}) - cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble','design','sets','groupmode']}) + cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','count','diffs','group','processors','topdown']}) + cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble','design','sets','groupmode','subsample','subsampleiters']}) cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']}) - cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design']}) - cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) + cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design','count']}) + cmd_dict['remove.lineage'] = dict({'required' : [['taxonomy','constaxonomy'],'taxon'],'optional' : ['fasta','name','group','list','alignreport','dups','shared','list','count']}) cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) - cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) - cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) + cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup','count']}) + cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups','count','fastq']}) cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) - cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','taxonomy','processors']}) + cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','taxonomy','processors','count','summary','contigsreport']}) cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']}) cmd_dict['seq.error'] = dict({'required' : ['fasta','reference'] , 'optional' : ['name','qfile','report','ignorechimeras','threshold','processors']}) - cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) + cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','fasta','qfile','trim','sfftxt','flow','accnos']}) cmd_dict['shhh.flows'] = dict({'required' : [['flow']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','large','processors']}) cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','name']], 'optional' : ['group','sigma','processors']}) - cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) - cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']}) - cmd_dict['sort.seqs'] = dict({'required' : [['fasta','qfile','name','group','flow','taxonomy']], 'optional' : ['accnos','large']}) - cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) - cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name']}) - cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']}) - cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']}) - cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']}) - cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy']}) - cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label','subsample','iters','processors']}) + cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list','count']], 'optional' : ['cutoff','group','groups','label','accnos']}) + cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups','count']}) + cmd_dict['sort.seqs'] = dict({'required' : [['fasta','qfile','name','group','flow','taxonomy']], 'optional' : ['accnos','large','count']}) + cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample','count','taxonomy']}) + cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name','count']}) + cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors','count']}) + cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors','subsample','iters']}) + cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode','subsample','iters']}) + cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy','count','relabund']}) + cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label','subsample','iters','processors','count']}) cmd_dict['trim.flows'] = dict({'required' : ['flow'], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','minflows','maxflows','fasta','signal','noise','maxhomop','order','processors']}) - cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','keepforward','allfiles','keepfirst','removelast','processors']}) - cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']}) - cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']}) - cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']}) - cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize']}) + cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','keepforward','allfiles','keepfirst','removelast','processors','count','checkorient','logtransform']}) + cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors','count']}) + cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors','count']}) + cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','count']}) + cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize','sharedotus']}) + + cmd_dict['merge.sfffiles'] = dict({'required' : ['sff','output']}) parser = optparse.OptionParser() # Options for managing galaxy interaction @@ -405,7 +408,7 @@ parser.add_option( '--report', dest='report', help='' ) parser.add_option( '--taxonomy', dest='taxonomy', help='A Taxonomy file' ) parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' ) - parser.add_option( '--contaxonomy', dest='contaxonomy', help='The Taxonomy file output by classify.otu' ) + parser.add_option( '--constaxonomy', dest='constaxonomy', help='The Taxonomy file output by classify.otu' ) parser.add_option( '--taxon', dest='taxon', help='A Taxon' ) parser.add_option( '--taxlevel', dest='taxlevel', type="int", help='A Taxonomy level' ) # parser.add_option( '--taxon', dest='taxon', action="callback", callback=remove_confidence_callback, help='A Taxon' ) @@ -532,6 +535,7 @@ parser.add_option( '--persample', dest='persample', help='sub sample option' ) parser.add_option( '--timing', dest='timing', help='timing option' ) parser.add_option( '--processors', dest='processors', type='int', action='callback', callback=processors_callback, help='Number of processors to use' ) + parser.add_option( '--dereplicate', dest='dereplicate', help='Boolean - remove chimeric sequences from all groups, default=f') parser.add_option( '--abskew', dest='abskew', type="float", help='Minimum abundance skew.') parser.add_option( '--chimealns', dest='chimealns', help='Boolean - produce a file containing multiple alignments of query sequences') parser.add_option( '--minh', dest='minh', type="float", help='mininum score to report chimera.') @@ -568,11 +572,20 @@ # include read.tree options parser.add_option( '--tree', dest='tree', help='' ) + # trim.seq options + parser.add_option( '--checkorient', dest='checkorient', help='' ) + parser.add_option( '--logtransform', dest='logtransform', help='' ) + #fastq.info options + parser.add_option( '--format', dest='format', help='' ) + parser.add_option( '--pacbio', dest='pacbio', help='' ) + parser.add_option( '--picrust', dest='picrust', help='' ) + parser.add_option( '--subsampleiters', dest='subsampleiters', help='' ) + (options, args) = parser.parse_args() """ """ # print >> sys.stderr, options # so will appear as blurb for file - if options.debug != None: + if debug == None and options.debug != None: debug = options.debug params = [] inputdir = None @@ -658,20 +671,26 @@ tmp_stderr.close() tmp_stdout.close() if debug: print >> sys.stdout, 'parse %s' % tmp_stdout_name + if returncode != 0: - try: - # try to copy stdout to the logfile - for output in options.result.split(','): - # Each item has a regex pattern and a file path to a galaxy dataset - (pattern,path) = output.split(':') - if debug: print >> sys.stdout, '%s -> %s' % (pattern,path) - if pattern.find('\.logfile') > 0: - if path != None and os.path.exists(path): - logfile_to_html(tmp_stdout_name,path,inputdir,outputdir,title="Mothur %s Error Logfile" % options.cmd) - break - except: - pass - raise Exception, stderr + if returncode == -11 and options.cmd == 'seq.error': + if debug: print >> sys.stdout, 'seq.error produced a segmentation fault but we are ignoring it.' + else: + try: + # try to copy stdout to the logfile + for output in options.result.split(','): + # Each item has a regex pattern and a file path to a galaxy dataset + (pattern,path) = output.split(':') + if debug: print >> sys.stdout, '%s -> %s' % (pattern,path) + if pattern.find('\.logfile') > 0: + if path != None and os.path.exists(path): + logfile_to_html(tmp_stdout_name,path,inputdir,outputdir,title="Mothur %s Error Logfile" % options.cmd) + break + except: + pass + + raise Exception, stderr + " Return code: " + str(returncode) + stdout = '' # Parse stdout to provide info tmp_stdout = open( tmp_stdout_name, 'rb' ) @@ -713,7 +732,7 @@ continue if line.find(outputdir) >= 0: continue - if line.startswith('**************'): + if line.startswith('**************'): continue if re.match('^Processing.*',line): continue @@ -733,7 +752,7 @@ continue if re.match('Output .*',line): break - if re.match('mothur > quit()',line): + if re.match('mothur > quit()',line): break if found_begin and info_chars < 200: info += "%s" % line
--- a/mothur/tools/mothur/nmds.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/nmds.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_nmds" name="Nmds" version="1.19.0"> +<tool id="mothur_nmds" name="Nmds" version="1.20.0"> <description>generate non-metric multidimensional scaling data</description> <command interpreter="python"> mothur_wrapper.py @@ -41,7 +41,7 @@ <data format="tabular" name="stress_nmds" label="${tool.name} on ${on_string}: nmds.stress"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -61,6 +61,7 @@ .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _nmds: http://www.mothur.org/wiki/Nmds +v1.20.0: Updated to mothur 1.33 </help> </tool>
--- a/mothur/tools/mothur/normalize.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/normalize.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_normalize_shared" name="Normalize.shared" version="1.20.0"> +<tool id="mothur_normalize_shared" name="Normalize.shared" version="1.21.0"> <description>Normalize the number of sequences per group to a specified level</description> <command interpreter="python"> mothur_wrapper.py @@ -50,7 +50,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: norm.shared" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/otu.association.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/otu.association.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_otu_association" name="Otu.association" version="1.24.0" force_history_refresh="True"> +<tool id="mothur_otu_association" name="Otu.association" version="1.25.0" force_history_refresh="True"> <description>Calculate the correlation coefficient for the otus</description> <command interpreter="python"> mothur_wrapper.py @@ -24,6 +24,10 @@ #if $metadata.__str__ != "None" and len($method.__str__) > 0: --metadata=$metadata #end if + #if $cutoff.__str__ != '': + --cutoff=$cutoff + #end if + </command> <inputs> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> @@ -43,12 +47,13 @@ <option value="kendall">kendall</option> </param> <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/> + <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -69,5 +74,7 @@ .. _relabund: http://www.mothur.org/wiki/Get.relabund .. _otu.association: http://www.mothur.org/wiki/Otu.association +v.1.25.0: Updated to mothur 1.33, added cutoff option + </help> </tool>
--- a/mothur/tools/mothur/otu.hierarchy.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/otu.hierarchy.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.19.0"> +<tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.20.0"> <description>Relate OTUs at different distances</description> <command interpreter="python"> mothur_wrapper.py @@ -33,7 +33,7 @@ <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pairwise.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/pairwise.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.19.0"> +<tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.20.0"> <description>calculate uncorrected pairwise distances between sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -74,7 +74,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/parse.list.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/parse.list.xml Fri Oct 31 15:09:32 2014 -0400 @@ -12,6 +12,9 @@ #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <param name="otu" type="data" format="list" label="list - OTU List"/> @@ -22,12 +25,13 @@ <filter type="data_meta" ref="otu" key="labels" /> </options> </param> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -48,5 +52,7 @@ .. _group: http://www.mothur.org/wiki/Group_file .. _parse.list: http://www.mothur.org/wiki/Parse.list +v.1.19.0: Updated to mothur 1.33, added count parameter + </help> </tool>
--- a/mothur/tools/mothur/parsimony.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/parsimony.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_parsimony" name="Parsimony" version="1.19.0"> +<tool id="mothur_parsimony" name="Parsimony" version="1.20.0"> <description>Describes whether two or more communities have the same structure</description> <command interpreter="python"> mothur_wrapper.py @@ -19,6 +19,9 @@ --iters=$iters #end if --processors=8 + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/> @@ -34,6 +37,7 @@ <!-- random uses input prompts, not sure how to model that <param name="random" type="text" value="" label="random - The root name for random tests"/> --> +<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -47,7 +51,7 @@ --> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -66,6 +70,8 @@ .. _parsimony: http://www.mothur.org/wiki/Parsimony +v.1.20.0: Added count parameter + </help> </tool>
--- a/mothur/tools/mothur/pca.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/pca.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_pca" name="Pca" version="1.20.0"> +<tool id="mothur_pca" name="Pca" version="1.21.0"> <description>Principal Coordinate Analysis for a shared file</description> <command interpreter="python"> mothur_wrapper.py @@ -40,7 +40,7 @@ <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pcoa.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/pcoa.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_pcoa" name="Pcoa" version="1.19.0" > +<tool id="mothur_pcoa" name="Pcoa" version="1.20.0" > <description>Principal Coordinate Analysis for a distance matrix</description> <command interpreter="python"> mothur_wrapper.py @@ -18,7 +18,7 @@ <data format="tabular" name="loadings" label="${tool.name} on ${on_string}: loadings" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pcr.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/pcr.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_pcr_seqs" name="Pcr.seqs" version="1.25.0"> +<tool id="mothur_pcr_seqs" name="Pcr.seqs" version="1.26.0"> <description>Trim sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -39,6 +39,9 @@ $keepdots --result=#echo ','.join($results) --processors=8 + #if $pdiffs.__str__ != '' and int($pdiffs.__str__) > 0: + --pdiffs=$pdiffs + #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> @@ -81,7 +84,9 @@ <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequence representative name list"/> <param name="group_in" type="data" format="groups" optional="true" label="group - Group file"/> - + <param name="pdiffs" type="integer" value="0" label="pdiffs - number of differences to allow in the primer (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -99,7 +104,7 @@ </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/phylo.diversity.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/phylo.diversity.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.20.0"> +<tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.21.0"> <description>Alpha Diversity calculates unique branch length</description> <command interpreter="python"> mothur_wrapper.py @@ -30,6 +30,9 @@ $summary #end if --processors=8 + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <!-- list,group or shared --> @@ -56,6 +59,7 @@ <param name="rarefy" type="boolean" truevalue="--rarefy=true" falsevalue="" checked="false" label="rarefy - Calculate the rarefaction data" /> <param name="summary" type="boolean" truevalue="" falsevalue="--summary=false" checked="true" label="summary - Generate a summary file" /> <param name="collect" type="boolean" truevalue="--collect=true" falsevalue="" checked="false" label="collect - Create a collectors curve" /> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -74,7 +78,7 @@ --> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -93,6 +97,8 @@ .. _phylo.diversity: http://www.mothur.org/wiki/Phylo.diversity +v.1.21.0: Updated to Mothur 1.33, added count parameter + </help> </tool>
--- a/mothur/tools/mothur/phylotype.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/phylotype.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_phylotype" name="Phylotype" version="1.19.0"> +<tool id="mothur_phylotype" name="Phylotype" version="1.20.0"> <description>Assign sequences to OTUs based on taxonomy</description> <command interpreter="python"> mothur_wrapper.py @@ -41,7 +41,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pre.cluster.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/pre.cluster.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.23.0"> +<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.24.0"> <description>Remove sequences due to pyrosequencing errors</description> <command interpreter="python"> mothur_wrapper.py @@ -10,10 +10,12 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.precluster.map',$os.path.basename($fasta.__str__)) + ":'" + $map_out.__str__] --cmd='pre.cluster' --outputdir='$logfile.extra_files_path' - --fasta=$fasta - #if $name.__str__ != "None" and len($name.__str__) > 0: + --fasta=$fasta + #if isinstance($name.datatype, $__app__.datatypes_registry.get_datatype_by_extension('name').__class__): --name=$name - #end if + #else + --count=$name + #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group=$group #end if @@ -22,12 +24,14 @@ #end if --result=#echo ','.join($results) --processors=8 + --topdown </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/> - <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> + <param name="name" type="data" format="names,count_table" optional="true" label="name - Sequences Name reference"/> <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference"/> <param name="diffs" type="integer" value="1" label="diffs - Number of mismatched bases to allow between sequences in a group (default 1)"/> +<param name="topdown" type="boolean" truevalue="--topdown=true" falsevalue="" checked="false" label="allows you to specify whether to cluster from largest abundance to smallest or vice versa. Default =T, which is largest to smallest"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -36,7 +40,7 @@ <data format="tabular" name="map_out" label="${tool.name} on ${on_string}: precluster.map" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -55,6 +59,7 @@ .. _pre.cluster: http://www.mothur.org/wiki/Pre.cluster +v1.24.0: Updated to mothur 1.33, added count and topdown parameter </help> </tool>
--- a/mothur/tools/mothur/rarefaction.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/rarefaction.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.26.0" force_history_refresh="True"> +<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.27.0" force_history_refresh="True"> <description>Generate inter-sample rarefaction curves for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -12,20 +12,20 @@ #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if - #if $design.use: - --design=$design.design - #if $design.sets.__str__ != '': - --sets='$design.sets' + #if $designc.use: + --design=$designc.design + #if $designc.sets.__str__ != '': + --sets='$designc.sets' #end if #end if #if int($iters.__str__) > 0: --iters=$iters - #end if + #end if $jumble #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if - #if $subsample.use.__str__ == 'yes': + #if $subsample.use: #if $subsample.subsample.__str__ != '': --subsample=$subsample.subsample #else @@ -54,7 +54,7 @@ --> </options> </param> - <conditional name="design"> + <conditional name="designc"> <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label=" run on a per set basis using a design file"/> <when value="yes"> <param name="design" type="data" format="design" label="design - assigns groups to sets" @@ -82,7 +82,7 @@ <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/> </when> <when value="no"/> - </conditional> + </conditional> </inputs> <outputs> @@ -90,7 +90,7 @@ <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/rarefaction.single.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/rarefaction.single.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.21.0" force_history_refresh="True"> <description>Generate intra-sample rarefaction curves for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -69,7 +69,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> @@ -78,7 +78,7 @@ Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. +provides bioinformatics for the microbial ecology community .. _Mothur: http://www.mothur.org/wiki/Main_Page
--- a/mothur/tools/mothur/remove.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/remove.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_remove_groups" name="Remove.groups" version="1.24.0"> +<tool id="mothur_remove_groups" name="Remove.groups" version="1.25.0"> <description>Remove groups from groups,fasta,names,list,taxonomy</description> <command interpreter="python"> mothur_wrapper.py @@ -7,8 +7,12 @@ ## adds .pick before the last extension to the input file #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] --cmd='remove.groups' - --outputdir='$logfile.extra_files_path' - --group=$group_in + --outputdir='$logfile.extra_files_path' + #if isinstance($group_in.datatype, $__app__.datatypes_registry.get_datatype_by_extension('group').__class__): + --group=$group_in + #else + --count=$group_in + #end if #if $groupnames.source == 'groups': #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: --groups=$groupnames.groups @@ -45,7 +49,7 @@ --result=#echo ','.join($results) </command> <inputs> - <param name="group_in" type="data" format="groups" label="group - Groups"/> + <param name="group_in" type="data" format="groups,count_table" label="group - Groups"/> <conditional name="groupnames"> <param name="source" type="select" label="Select Group Names from"> <option value="groups">A List of Group Names</option> @@ -94,7 +98,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.lineage.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/remove.lineage.xml Fri Oct 31 15:09:32 2014 -0400 @@ -5,10 +5,17 @@ #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pick before the last extension to the input file - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] --cmd='remove.lineage' - --outputdir='$logfile.extra_files_path' - --taxonomy=$taxonomy + --outputdir='$logfile.extra_files_path' + #if $file.filetype.__str__ == "usetaxonomy" + --taxonomy=$file.taxonomy + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] + #else + --constaxonomy=$file.constaxonomy + --shared=$file.shared + --list=$file.list + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy.__str__)) + ":'" + $taxonomy_out.__str__] + #end if --taxon="'$re.sub('(\s|,)+',',',$re.sub('\(\d+\)','',$taxon.value.__str__))'" #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: --fasta=$fasta_in @@ -28,13 +35,29 @@ #end if #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: --name=$name_in - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] $dups #end if --result=#echo ','.join($results) + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> - <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> + <conditional name ="file"> + <param name = "filetype" type = "select" label="choose which file is used"> + <option value = "usetaxonomy" selected = "true">taxonomy</option> + <option value = "useconstaxonomy">constaxonomy</option> + </param> + <when value = "usetaxonomy"> + <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> + </when> + <when value = "useconstaxonomy"> + <param name="constaxonomy" type="data" format="cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file"/> + <param name="shared" type="data" format="shared" label="shared - shared file" optional="true"/> + <param name="list" type="data" format="list" label="list - list file" optional="true"/> + </when> + </conditional> <!-- <param name="taxons" type="select" size="120" multiple="true" label="Browse Taxons from Taxonomy"> <options from_dataset="taxonomy"> @@ -52,6 +75,7 @@ <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -73,7 +97,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.otulabels.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/remove.otulabels.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_remove_otulabels" name="Remove.otulabels" version="1.26.0"> +<tool id="mothur_remove_otulabels" name="Remove.otulabels" version="1.27.0"> <description>Removes OTU labels</description> <command interpreter="python"> mothur_wrapper.py @@ -21,12 +21,20 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($corraxes_in.__str__)) + ":'" + $corraxes_out.__str__] #end if --result=#echo ','.join($results) + #if $list.__str__ != "None" and len($list.__str__) > 0: + --list='$list' + #end if + #if $shared.__str__ != "None" and len($shared.__str__) > 0: + --shared='$shared' + #end if </command> <inputs> <param name="accnos" type="data" format="otulabels" label="accnos - otulabels"/> <param name="constaxonomy_in" type="data" format="cons.taxonomy" optional="true" label="constaxonomy - Consensus Taxonomy from classify.otu"/> <param name="otucorr_in" type="data" format="otu.corr" optional="true" label="otucorr - OTU correlation from otu.association"/> <param name="corraxes_in" type="data" format="axes" optional="true" label="corraxes - axes from corr.axes"/> + <param name="list" type="data" format="list" optional="true" label="list - allows you to input a list parameter to select OTUs from"/> + <param name="shared" type="data" format="shared" optional="true" label="shared - input a shared file to select OTUs from"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -43,7 +51,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.otus.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/remove.otus.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_remove_otus" name="Remove.otus" version="1.19.0"> +<tool id="mothur_remove_otus" name="Remove.otus" version="1.20.0"> <description>Remove otus containing sequences from specified groups</description> <command interpreter="python"> mothur_wrapper.py @@ -55,7 +55,7 @@ <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.rare.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/remove.rare.xml Fri Oct 31 15:09:32 2014 -0400 @@ -35,7 +35,10 @@ --label=$input.label #end if --nseqs=$nseqs - --result=#echo ','.join($results) + --result=#echo ','.join($results) + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <conditional name="input"> @@ -80,7 +83,8 @@ </options> </param> </when> - </conditional> + </conditional> + <param name = "count" type = "data" format = "count_table" optional = "true" label="count" help ="If you clustered with a count file, be sure to include it"/> <param name="nseqs" type="integer" value="1" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> </inputs> <outputs> @@ -91,7 +95,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/remove.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_remove_seqs" name="Remove.seqs" version="1.20.0"> +<tool id="mothur_remove_seqs" name="Remove.seqs" version="1.21.0"> <description>Remove sequences by name</description> <command interpreter="python"> mothur_wrapper.py @@ -38,6 +38,13 @@ #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] #end if --result=#echo ','.join($results) + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + #if $fastq.__str__ != "None" and len($fastq.__str__) > 0: + --fastq=$fastq + #end if + </command> <inputs> <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/> @@ -49,6 +56,8 @@ <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name="fastq" type="data" format="fastq" optional="true" label="fastq" /> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -77,7 +86,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/reverse.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/reverse.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_reverse_seqs" name="Reverse.seqs" version="1.19.0"> +<tool id="mothur_reverse_seqs" name="Reverse.seqs" version="1.20.0"> <description>Reverse complement the sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -15,7 +15,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: rc.fasta" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/screen.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/screen.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.23.0"> +<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.24.0"> <description>Screen sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -57,6 +57,17 @@ #end if --result=#echo ','.join($results) --processors=8 + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + #if $summary != None and $summary.__str__ != "None": + --summary=$summary + #end if + #if $contigsreport != None and $contigsreport.__str__ != "None": + --contigsreport=$contigsreport + #end if + + </command> <inputs> <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/> @@ -79,7 +90,10 @@ <param name="input_names" type="data" format="names" optional="true" label="name - Sequence Names to screen"/> <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/> <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/> + <param name="summary" type="data" format="synnary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/> + <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/> <param name="input_taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -102,7 +116,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sens.spec.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/sens.spec.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_sens_spec" name="Sens.spec" version="1.19.0" > +<tool id="mothur_sens_spec" name="Sens.spec" version="1.20.0" > <description>Determine the quality of OTU assignment</description> <command interpreter="python"> mothur_wrapper.py @@ -42,7 +42,7 @@ <data format="tabular" name="sensspec" label="${tool.name} on ${on_string}: sensspec" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/seq.error.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/seq.error.xml Fri Oct 31 15:09:32 2014 -0400 @@ -54,6 +54,9 @@ $ignorechimeras --result=#echo ','.join($results) --processors=8 + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count='$count' + #end if </command> <inputs> <param name="fasta_in" type="data" format="align" label="fasta - Candiate Sequences"/> @@ -64,9 +67,7 @@ </param> <when value="ref"> <param name="template" type="select" label="reference - Select an alignment database " help=""> - <options from_file="mothur_aligndb.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_aligndb"> </options> </param> </when> @@ -88,7 +89,7 @@ </when> <when value="no"/> </conditional> - + <param name="count" type="data" format="count_table" optional="true" label="The count parameter allows you to provide a count file associated with your fasta file, so you can include the redundant sequences in your error analysis"/> <param name="threshold" type="float" value="" optional="true" label="threshold - error rate at which to report (default 1.)" help=""> <validator type="in_range" message="error rate threshold between 0. and 1." min="0.0" max="1.0"/> @@ -110,7 +111,7 @@ </param> </inputs> <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />}} <data format="tabular" name="summary_out" label="${tool.name} on ${on_string}: error.summary" > <filter>('summary' in output_sel)</filter> </data> @@ -146,7 +147,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sffinfo.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/sffinfo.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_sffinfo" name="Sffinfo" version="1.24.0"> +<tool id="mothur_sffinfo" name="Sffinfo" version="1.25.0"> <description>Summarize the quality of sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -14,6 +14,27 @@ #if $accnos.__str__ != 'None' and len($accnos.__str__) > 0: --accnos=$accnos #end if + + #if $oligo.add == "yes": + --oligos=$oligo.oligos + #if $oligo.bdiffs.__str__ != '' and int($oligo.bdiffs.__str__) > 0: + --bdiffs=$oligo.bdiffs + #end if + #if $oligo.pdiffs.__str__ != '' and int($oligo.pdiffs.__str__) > 0: + --pdiffs=$oligo.pdiffs + #end if + #if $oligo.tdiffs.__str__ != '' and int($oligo.tdiffs.__str__) > 0: + --tdiffs=$oligo.tdiffs + #end if + #if $oligo.ldiffs.__str__ != '' and int($oligo.ldiffs.__str__) > 0: + --ldiffs=$oligo.ldiffs + #end if + #if $oligo.sdiffs.__str__ != '' and int($oligo.sdiffs.__str__) > 0: + --sdiffs=$oligo.sdiffs + #end if + --datasetid='$sffinfo.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow' + #end if </command> <inputs> <param name="sff" type="data" format="sff" label="sff - Sff data"/> @@ -30,6 +51,39 @@ <option value="flow">flow</option> </param> --> + + + <conditional name="oligo"> + <param name="add" type="select" label="Trim with an oligos file?" + help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. + Each line of the oligos file can start with the key words "forward", "reverse", + and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file. "> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="oligos" type="data" format="oligos" label="oligos - barcodes and primers"/> + <param name="bdiffs" type="integer" value="0" label="bdiffs - number of differences to allow in the barcode (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="pdiffs" type="integer" value="0" label="pdiffs - number of differences to allow in the primer (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="tdiffs" type="integer" value="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="ldiffs" type="integer" value="0" optional="true" label="ldiffs - total number of differences to allow in linker sequence (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + <param name="sdiffs" type="integer" value="0" optional="true" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"> + <validator type="in_range" message="Number of differences can't be negative" min="0"/> + </param> + </when> + </conditional> + + + <param name="fasta" type="boolean" truevalue="" falsevalue="--fasta=false" checked="true" label="fasta - Add fasta to your history" /> <param name="qfile" type="boolean" truevalue="" falsevalue="--qfile=false" checked="true" label="qfile - Add qfile to your history" /> <param name="sfftxt" type="boolean" truevalue="--sfftxt=true" falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history" /> @@ -53,7 +107,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/shhh.flows.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/shhh.flows.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_shhh_flows" name="Shhh.flows" version="1.26.0" force_history_refresh="True"> +<tool id="mothur_shhh_flows" name="Shhh.flows" version="1.27.0" force_history_refresh="True"> <description>Denoise flowgrams (PyroNoise algorithm)</description> <command interpreter="python"> mothur_wrapper.py @@ -39,9 +39,7 @@ <when value="ref"> <param name="lookup" type="select" format="tabular" label="lookup - intensity value per homopolymer length" help="table of the probability of observing an intensity value for a given homopolymer length"> - <options from_file="mothur_lookup.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_lookup"> </options> </param> </when> @@ -70,8 +68,8 @@ <validator type="in_range" message="sigma between 0. and 1." min="0.0" max="1.0"/> </param> - <param name="order" type="text" value="" label="order - flow order for nucleotides in the sequencer" - help="default is TACG"/> + <param name="order" type="text" value="A" label="order - flow order for nucleotides in the sequencer" + help="default is A, was TACG. Also accepts B or I"/> <param name="large" type="integer" value="10000" optional="true" label="large - split your flow file and process the pieces separately (default 10000)" help=""> <validator type="in_range" message="large value must be positive" min="1"/> @@ -86,7 +84,7 @@ <data format="tabular" name="shhh_counts" label="${tool.name} on ${on_string}: shhh.counts"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/shhh.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/shhh.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_shhh_seqs" name="Shhh.seqs" version="1.23.0"> +<tool id="mothur_shhh_seqs" name="Shhh.seqs" version="1.24.0"> <description>Denoise program (Quince SeqNoise)</description> <command interpreter="python"> mothur_wrapper.py @@ -32,7 +32,7 @@ <data format="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sort.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/sort.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_sort_seqs" name="Sort.seqs" version="1.24.0"> +<tool id="mothur_sort_seqs" name="Sort.seqs" version="1.25.0"> <description>put sequences in different files in the same order</description> <command interpreter="python"> mothur_wrapper.py @@ -36,6 +36,9 @@ #end if $large --result=#echo ','.join($results) +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if </command> <inputs> <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences"/> @@ -46,6 +49,7 @@ <param name="taxonomy_in" type="select" format="seq.taxonomy" optional="true" label="taxonomy - taxonomy reference"/> <param name="accnos" type="data" format="accnos" optional="true" label="accnos - sort "/> <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Datasets are large and may not fit in RAM"/> +<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -69,7 +73,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/split.abund.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/split.abund.xml Fri Oct 31 15:09:32 2014 -0400 @@ -29,6 +29,8 @@ #if $accnos: #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.accnos)$',$os.path.basename($search.input.__str__)) + ":accnos'"] #end if + #else + --count=$search.input #end if --cutoff=$cutoff #if $split.type == 'yes': @@ -52,6 +54,7 @@ <param name="type" type="select" label="Type to screen" help=""> <option value="list">OTU List</option> <option value="name">Name reference</option> + <option value="count">Count file</option> </param> <when value="name"> <param name="input" type="data" format="names" label="name - Name reference"/> @@ -64,6 +67,9 @@ </options> </param> </when> + <when value = "count"> + <param name="input" type="data" format="count_table" label="count - count_table file"/> + </when> </conditional> <!-- search --> <param name="cutoff" type="integer" value="10" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/> <conditional name="split"> @@ -98,7 +104,7 @@ --> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/split.groups.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/split.groups.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_split_groups" name="Split.groups" version="1.20.0" force_history_refresh="True"> +<tool id="mothur_split_groups" name="Split.groups" version="1.21.0" force_history_refresh="True"> <description>Generates a fasta file for each group</description> <command interpreter="python"> mothur_wrapper.py @@ -15,6 +15,9 @@ #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/> @@ -25,12 +28,13 @@ <filter type="data_meta" ref="group" key="groups" /> </options> </param> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sub.sample.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/sub.sample.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_sub_sample" name="Sub.sample" version="1.22.0"> +<tool id="mothur_sub_sample" name="Sub.sample" version="1.23.0"> <description>Create a sub sample</description> <command interpreter="python"> mothur_wrapper.py @@ -66,6 +66,12 @@ --size=$size #end if --result=#echo ','.join($results) + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + #if $taxonomy.__str__ != "None" and len($taxonomy.__str__) > 0: + --taxonomy=$taxtaxonomy + #end if </command> <inputs> <conditional name="input"> @@ -151,6 +157,8 @@ </when> <!-- rabund --> </conditional> <!-- input --> <param name="size" type="integer" value="0" label="size - If greater than 0, the number of samples to pick"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -179,7 +187,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.qual.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/summary.qual.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_summary_qual" name="Summary.qual" version="1.23.0"> +<tool id="mothur_summary_qual" name="Summary.qual" version="1.24.0"> <description>Summarize the quality scores</description> <command interpreter="python"> mothur_wrapper.py @@ -10,17 +10,21 @@ --name=$name #end if ## --processors=8 +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if </command> <inputs> <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> <param name="name" type="data" format="names" optional="true" label="name - Names"/> +<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/summary.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_summary_seqs" name="Summary.seqs" version="1.19.0"> +<tool id="mothur_summary_seqs" name="Summary.seqs" version="1.20.0"> <description>Summarize the quality of sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -9,18 +9,25 @@ #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if + + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + --processors=8 </command> <inputs> <param name="fasta" type="data" format="fasta,align" label="fasta - Dataset"/> <param name="name" type="data" format="names" label="name - Names" optional="true"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" + help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/summary.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_summary_shared" name="Summary.shared" version="1.26.0" force_history_refresh="True"> +<tool id="mothur_summary_shared" name="Summary.shared" version="1.27.0" force_history_refresh="True"> <description>Summary of calculator values for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -121,7 +121,7 @@ <data format="tabular" name="summary" label="${tool.name} on ${on_string}: shared.summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.single.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/summary.single.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_summary_single" name="Summary.single" version="1.19.0" force_history_refresh="True"> +<tool id="mothur_summary_single" name="Summary.single" version="1.20.0" force_history_refresh="True"> <description>Summary of calculator values for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -107,7 +107,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.tax.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/summary.tax.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_summary_tax" name="Summary.tax" version="1.22.0"> +<tool id="mothur_summary_tax" name="Summary.tax" version="1.23.0"> <description>Assign sequences to taxonomy</description> <command interpreter="python"> mothur_wrapper.py @@ -15,6 +15,10 @@ #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: --reftaxonomy=$reftax.taxonomy #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if + $relabund </command> <inputs> <conditional name="tax"> @@ -24,9 +28,7 @@ </param> <when value="ref"> <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"> - <options from_file="mothur_taxonomy.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_taxonomy"> </options> </param> </when> @@ -45,9 +47,7 @@ <when value="none"/> <when value="ref"> <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"> - <options from_file="mothur_taxonomy.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> + <options from_data_table="mothur_taxonomy"> </options> </param> </when> @@ -55,13 +55,15 @@ <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/> </when> </conditional> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> +<param name="relabund" type="boolean" falsevalue="" truevalue="--relabund=true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/tree.shared.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/tree.shared.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_tree_shared" name="Tree.shared" version="1.25.0" force_history_refresh="True"> +<tool id="mothur_tree_shared" name="Tree.shared" version="1.26.0" force_history_refresh="True"> <description>Generate a newick tree for dissimilarity among groups</description> <command interpreter="python"> mothur_wrapper.py @@ -37,6 +37,8 @@ #if $input.name.__str__ != "None" and len($input.name.__str__) > 0: --name=$input.name #end if + #else + --count=$input.name #end if #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: @@ -51,6 +53,7 @@ <option value="shared">OTU Shared</option> <option value="column">Pairwise Column Distance Matrix</option> <option value="phylip">Phylip Distance Matrix</option> + <option value="count">Count file</option> </param> <when value="column"> <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> @@ -84,7 +87,11 @@ </when> <when value="no"/> </conditional> <!-- subsampling --> - </when> + </when> + <when value = "count"> + <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> + <param name="name" type="data" format="count" label="count - count_table file"/> + </when> </conditional> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> @@ -136,7 +143,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/trim.flows.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/trim.flows.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_trim_flows" name="Trim.flows" version="1.22.0" force_history_refresh="True"> +<tool id="mothur_trim_flows" name="Trim.flows" version="1.23.0" force_history_refresh="True"> <description>partition by barcode, trim to length, cull by lenght and mismatches</description> <command interpreter="python"> mothur_wrapper.py @@ -97,8 +97,8 @@ help="default .7"> <validator type="in_range" message="signal between 0. and 1." min="0.0" max="1.0"/> </param> - <param name="order" type="text" value="" label="order - flow order for nucleotides in the sequencer" - help="default is TACG"/> + <param name="order" type="text" value="A" label="order - flow order for nucleotides in the sequencer" + help="default is A, was TACG. Also accepts B or I"/> <param name="fasta" type="boolean" truevalue="--fasta=true" falsevalue="" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/> @@ -115,7 +115,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/trim.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/trim.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_trim_seqs" name="Trim.seqs" version="1.24.0" force_history_refresh="True"> +<tool id="mothur_trim_seqs" name="Trim.seqs" version="1.25.0" force_history_refresh="True"> <description>Trim sequences - primers, barcodes, quality</description> <command interpreter="python"> mothur_wrapper.py @@ -74,6 +74,12 @@ #if $names.__str__ != "None" and len($names.__str__) > 0: --name=$names #end if + + $logtransform + $checkorient + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if --processors=8 </command> <inputs> @@ -132,6 +138,16 @@ </when> </conditional> <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - reverse complement the trimmed sequences"/> + + + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" + help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/> + <param name="logtransform" type="boolean" truevalue="--logtransform=true" falsevalue="" checked="false" + label="logtransform - allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/> + <param name="checkorient" type="boolean" truevalue="--checkorient=true" falsevalue="" checked="false" + label="checkorient - If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/> + + </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -154,7 +170,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unifrac.unweighted.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/unifrac.unweighted.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.25.0"> +<tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.26.0"> <description>Describes whether two or more communities have the same structure</description> <command interpreter="python"> mothur_wrapper.py @@ -41,6 +41,9 @@ $root --result=#echo ','.join($results) --processors=1 +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if </command> <inputs> <param name="tree" type="data" format="tre" label="tree - Tree"/> @@ -73,6 +76,7 @@ <option value="column">Pairwise Distance Matrix</option> </param> <param name="root" type="boolean" truevalue="--root=true" falsevalue="" checked="false" label="root - the entire root in your calculations" /> +<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -110,7 +114,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unifrac.weighted.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/unifrac.weighted.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.25.0"> +<tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.26.0"> <description>Describes whether two or more communities have the same structure</description> <command interpreter="python"> mothur_wrapper.py @@ -41,6 +41,9 @@ $root --result=#echo ','.join($results) --processors=8 +#if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count +#end if </command> <inputs> <param name="tree" type="data" format="tre" label="tree - Tree"/> @@ -73,6 +76,7 @@ <option value="column">Pairwise Distance Matrix</option> </param> <param name="root" type="boolean" truevalue="--root=true" falsevalue="" checked="false" label="root - the entire root in your calculations" /> +<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -117,7 +121,7 @@ </data> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> +<requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unique.seqs.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/unique.seqs.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_unique_seqs" name="Unique.seqs" version="1.20.0"> +<tool id="mothur_unique_seqs" name="Unique.seqs" version="1.21.0"> <description>Return unique sequences</description> <command interpreter="python"> mothur_wrapper.py @@ -9,10 +9,17 @@ #if $names.__str__ != "None" and len($names.__str__) > 0: --name=$names #end if + + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> <param name="names" type="data" format="names" optional="true" label="names - Sequences Names"/> + + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" + help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information."/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -20,7 +27,7 @@ <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/venn.xml Mon Sep 22 11:19:09 2014 -0400 +++ b/mothur/tools/mothur/venn.xml Fri Oct 31 15:09:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_venn" name="Venn" version="1.23.0" force_history_refresh="True"> +<tool id="mothur_venn" name="Venn" version="1.24.0" force_history_refresh="True"> <description>Generate Venn diagrams for groups </description> <command interpreter="python"> mothur_wrapper.py @@ -37,6 +37,7 @@ #if 100 > $fontsize > 0: --fontsize=$fontsize #end if + $sharedotus </command> <inputs> <conditional name="input"> @@ -83,12 +84,13 @@ <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/> <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> + <param name="sharedotus" type="boolean" falsevalue="" truevalue="--sharedotus=true" checked="false" label="The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t."/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="package" version="1.27">mothur</requirement> + <requirement type="package" version="1.33">mothur</requirement> </requirements> <tests> </tests>