Mercurial > repos > jjohnson > mothur_toolsuite
changeset 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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--- a/mothur/README Wed May 16 13:12:05 2012 -0500 +++ b/mothur/README Tue Dec 04 11:05:19 2012 -0600 @@ -1,9 +1,15 @@ Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page -(The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands) +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 -Install mothur v.1.25.0 on your galaxy system so galaxy can execute the mothur command - ( This version of wrappers is designed for Mothur version 1.24 - it may work on later versions ) +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 ) 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 ) @@ -159,6 +165,134 @@ <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> <!-- End Mothur Datatypes --> +Reorganize integrated_tool_panel.xml : + <section id="metagenomics_mothur" name="Metagenomics Mothur" version=""> + <label text="Mothur Utilities" id="mothur_utilities"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_files/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_files/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_groups/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_groups/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_groups/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_groups/1.22.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_design/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sub_sample/1.22.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sort_seqs/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_create_database/1.27.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/CONVERTER_ref_to_seq_taxomony/1.0.0" /> + <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sffinfo/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_flows/1.26.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_flows/1.22.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_seqs/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_contigs/1.26.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_fastq/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_fastq_info/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_qual/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_reverse_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcr_seqs/1.25.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_seqs/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unique_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chop_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_screen_seqs/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_filter_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_degap_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_consensus_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_check/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pairwise_seqs/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_abund/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_groups/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcoa/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pca/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_nmds/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_corr_axes/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_seqs/1.21.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_seq_error/1.22.0" /> + <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_bellerophon/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_ccode/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_check/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_perseus/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_pintail/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_slayer/1.22.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_uchime/1.22.0" /> + <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pre_cluster/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_fragments/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster/1.27.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_hcluster/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_classic/1.27.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_split/1.27.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_metastats/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sens_spec/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_otu/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parse_list/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otus/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otus/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_rare/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulist/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_oturep/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_otulabels/1.26.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulabels/1.26.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otulabels/1.26.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_hierarchy/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_rabund/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sabund/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_relabund/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared/1.22.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared_from_biom/1.25.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_biom/1.25.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_group/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_bin_seqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sharedseqs/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_tax/1.22.0" /> + <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_single/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_single/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_single/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_bin/1.20.0" /> + <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_shared/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_shared/1.26.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_normalize_shared/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_shared/1.26.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_association/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_shared/1.25.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_sim/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_venn/1.23.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_tree_shared/1.25.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_coremicrobiome/1.26.0" /> + <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parsimony/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_weighted/1.25.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_unweighted/1.25.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_libshuff/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_amova/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_homova/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_mantel/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_anosim/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cooccurrence/1.25.0" /> + <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_lineage/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_lineage/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylotype/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylo_diversity/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_clearcut/1.19.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_indicator/1.21.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_tree/1.20.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_tree/1.24.0" /> + <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/tree_vector/1.0" /> + </section> + + + add mothur tools to: tool_conf.xml <section name="Metagenomics Mothur" id="metagenomics_mothur"> <label text="Mothur Utilities" id="mothur_utilities"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/datatypes_conf.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,90 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="metagenomics.py"/> + </datatype_files> + <registration> + <!-- 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="group.metadata" type="galaxy.datatypes.metagenomics:GroupMetadata" 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="otulabels" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/> + <datatype extension="otu.corr" type="galaxy.datatypes.tabular:Tabular" 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="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> + <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/> + <datatype extension="biom" type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix" display_in_upload="true"/> + <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"/> + <!-- End Mothur Datatypes --> + <!-- Start Qiime Datatypes --> + <datatype extension="qiimemapping" type="galaxy.datatypes.metagenomics:QiimeMetadataMapping" display_in_upload="true"/> + <datatype extension="qiimeotu" type="galaxy.datatypes.metagenomics:QiimeOTU" display_in_upload="true"/> + <datatype extension="qiimeotutable" type="galaxy.datatypes.metagenomics:QiimeOTUTable" display_in_upload="true"/> + <datatype extension="qiimedistmat" type="galaxy.datatypes.metagenomics:QiimeDistanceMatrix" display_in_upload="true"/> + <datatype extension="qiimetaxsummary" type="galaxy.datatypes.metagenomics:QiimeTaxaSummary" display_in_upload="true"/> + <datatype extension="qiimepca" type="galaxy.datatypes.metagenomics:QiimePCA" display_in_upload="true"/> + <datatype extension="qiimeparams" type="galaxy.datatypes.metagenomics:QiimeParams" display_in_upload="true"/> + <datatype extension="qiimeprefs" type="galaxy.datatypes.metagenomics:QiimePrefs" display_in_upload="true"/> + <!-- End Qiime Datatypes --> + </registration> + <sniffers> + <sniffer type="galaxy.datatypes.metagenomics:Otu"/> + <sniffer type="galaxy.datatypes.metagenomics:Sabund"/> + <sniffer type="galaxy.datatypes.metagenomics:GroupAbund"/> + <sniffer type="galaxy.datatypes.metagenomics:SharedRabund"/> + <sniffer type="galaxy.datatypes.metagenomics:RelAbund"/> + <sniffer type="galaxy.datatypes.metagenomics:SecondaryStructureMap"/> + <sniffer type="galaxy.datatypes.metagenomics:SequenceAlignment"/> + <sniffer type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:SquareDistanceMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:Oligos"/> + <sniffer type="galaxy.datatypes.metagenomics:Frequency"/> + <sniffer type="galaxy.datatypes.metagenomics:Quantile"/> + <sniffer type="galaxy.datatypes.metagenomics:LaneMask"/> + <sniffer type="galaxy.datatypes.metagenomics:RefTaxonomy"/> + <sniffer type="galaxy.datatypes.metagenomics:SequenceTaxonomy"/> + <sniffer type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy"/> + <sniffer type="galaxy.datatypes.metagenomics:Phylip"/> + <sniffer type="galaxy.datatypes.metagenomics:Axes"/> + <sniffer type="galaxy.datatypes.metagenomics:Newick"/> + <sniffer type="galaxy.datatypes.metagenomics:Nexus"/> + <sniffer type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:QiimeMetadataMapping"/> + </sniffers> +</datatypes>
--- a/mothur/lib/galaxy/datatypes/metagenomics.py Wed May 16 13:12:05 2012 -0500 +++ b/mothur/lib/galaxy/datatypes/metagenomics.py Tue Dec 04 11:05:19 2012 -0600 @@ -6,11 +6,7 @@ import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re import galaxy.model -from galaxy.datatypes import data from galaxy.datatypes.sniff import * -from galaxy.datatypes import metadata -from galaxy.datatypes import tabular -from galaxy.datatypes import sequence from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.data import Text from galaxy.datatypes.tabular import Tabular @@ -21,10 +17,8 @@ pkg_resources.require("simplejson") import simplejson - log = logging.getLogger(__name__) - ## Mothur Classes class Otu( Text ): @@ -833,6 +827,54 @@ close(fh) return False +class CountTable(Tabular): + MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + file_ext = 'count_table' + + def __init__(self, **kwd): + """ + A table with first column names and following columns integer counts + # Example 1: + Representative_Sequence total + U68630 1 + U68595 1 + U68600 1 + # Example 2 (with group columns): + Representative_Sequence total forest pasture + U68630 1 1 0 + U68595 1 1 0 + U68600 1 1 0 + U68591 1 1 0 + U68647 1 0 1 + """ + Tabular.__init__( self, **kwd ) + self.column_names = ['name','total'] + + def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): + try: + data_lines = 0; + fh = open( dataset.file_name ) + line = fh.readline() + if line: + line = line.strip() + colnames = line.split() + if len(colnames) > 1: + dataset.metadata.columns = len( colnames ) + if len(colnames) > 2: + dataset.metadata.groups = colnames[2:] + column_types = ['str'] + for i in range(1,len(colnames)): + column_types.append('int') + dataset.metadata.column_types = column_types + dataset.metadata.comment_lines = 1 + while line: + line = fh.readline() + if not line: break + data_lines += 1 + dataset.metadata.data_lines = data_lines + finally: + close(fh) + class RefTaxonomy(Tabular): file_ext = 'ref.taxonomy' """ @@ -1378,7 +1420,7 @@ MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) file_ext = 'qiimeotutable' def init_meta( self, dataset, copy_from=None ): - tabular.Tabular.init_meta( self, dataset, copy_from=copy_from ) + Tabular.init_meta( self, dataset, copy_from=copy_from ) def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): self.set_column_names(dataset) def set_column_names(self, dataset): @@ -1400,7 +1442,7 @@ """ file_ext = 'qiimedistmat' def init_meta( self, dataset, copy_from=None ): - tabular.Tabular.init_meta( self, dataset, copy_from=copy_from ) + Tabular.init_meta( self, dataset, copy_from=copy_from ) def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): self.set_column_names(dataset) def set_column_names(self, dataset):
--- a/mothur/tool-data/datatypes.conf.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tool-data/datatypes.conf.xml Tue Dec 04 11:05:19 2012 -0600 @@ -4,6 +4,7 @@ <datatype_file name="metagenomics.py"/> </datatype_files> <registration> + <!-- 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"/> @@ -12,11 +13,16 @@ <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="group.metadata" type="galaxy.datatypes.metagenomics:GroupMetadata" 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="otulabels" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/> + <datatype extension="otu.corr" type="galaxy.datatypes.tabular:Tabular" 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"/> @@ -26,7 +32,7 @@ <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"/> + <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"/> @@ -38,10 +44,47 @@ <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="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/> - <datatype extension="tre" type="galaxy.datatypes.metagenomics:Newick" display_in_upload="true"/> <datatype extension="biom" type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix" display_in_upload="true"/> <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"/> + <!-- End Mothur Datatypes --> + <!-- Start Qiime Datatypes --> + <datatype extension="qiimemapping" type="galaxy.datatypes.metagenomics:QiimeMetadataMapping" display_in_upload="true"/> + <datatype extension="qiimeotu" type="galaxy.datatypes.metagenomics:QiimeOTU" display_in_upload="true"/> + <datatype extension="qiimeotutable" type="galaxy.datatypes.metagenomics:QiimeOTUTable" display_in_upload="true"/> + <datatype extension="qiimedistmat" type="galaxy.datatypes.metagenomics:QiimeDistanceMatrix" display_in_upload="true"/> + <datatype extension="qiimetaxsummary" type="galaxy.datatypes.metagenomics:QiimeTaxaSummary" display_in_upload="true"/> + <datatype extension="qiimepca" type="galaxy.datatypes.metagenomics:QiimePCA" display_in_upload="true"/> + <datatype extension="qiimeparams" type="galaxy.datatypes.metagenomics:QiimeParams" display_in_upload="true"/> + <datatype extension="qiimeprefs" type="galaxy.datatypes.metagenomics:QiimePrefs" display_in_upload="true"/> + <!-- End Qiime Datatypes --> </registration> + <sniffers> + <sniffer type="galaxy.datatypes.metagenomics:Otu"/> + <sniffer type="galaxy.datatypes.metagenomics:Sabund"/> + <sniffer type="galaxy.datatypes.metagenomics:GroupAbund"/> + <sniffer type="galaxy.datatypes.metagenomics:SharedRabund"/> + <sniffer type="galaxy.datatypes.metagenomics:RelAbund"/> + <sniffer type="galaxy.datatypes.metagenomics:SecondaryStructureMap"/> + <sniffer type="galaxy.datatypes.metagenomics:SequenceAlignment"/> + <sniffer type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:SquareDistanceMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:Oligos"/> + <sniffer type="galaxy.datatypes.metagenomics:Frequency"/> + <sniffer type="galaxy.datatypes.metagenomics:Quantile"/> + <sniffer type="galaxy.datatypes.metagenomics:LaneMask"/> + <sniffer type="galaxy.datatypes.metagenomics:RefTaxonomy"/> + <sniffer type="galaxy.datatypes.metagenomics:SequenceTaxonomy"/> + <sniffer type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy"/> + <sniffer type="galaxy.datatypes.metagenomics:Phylip"/> + <sniffer type="galaxy.datatypes.metagenomics:Axes"/> + <sniffer type="galaxy.datatypes.metagenomics:Newick"/> + <sniffer type="galaxy.datatypes.metagenomics:Nexus"/> + <sniffer type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix"/> + <sniffer type="galaxy.datatypes.metagenomics:QiimeMetadataMapping"/> + </sniffers> </datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool_dependencies.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,38 @@ +<?xml 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> + <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">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the Mothur package in most environments . + +http://www.mothur.org/wiki/Download_mothur + +http://www.mothur.org/wiki/Installation + +http://www.mothur.org/wiki/Makefile_options + + </readme> + </package> + <!-- + http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip + --> +</tool_dependency> +
--- a/mothur/tools/mothur/align.check.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/align.check.xml Tue Dec 04 11:05:19 2012 -0600 @@ -33,7 +33,7 @@ <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/align.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/align.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -96,7 +96,7 @@ <data format="align.report" name="report" label="${tool.name} on ${on_string}: align.report" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/amova.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/amova.xml Tue Dec 04 11:05:19 2012 -0600 @@ -26,7 +26,7 @@ <data format="tabular" name="amova" label="${tool.name} on ${on_string}: amova"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/anosim.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/anosim.xml Tue Dec 04 11:05:19 2012 -0600 @@ -26,7 +26,7 @@ <data format="tabular" name="anosim" label="${tool.name} on ${on_string}: anosim"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/bin.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/bin.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -34,7 +34,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.bellerophon.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.bellerophon.xml Tue Dec 04 11:05:19 2012 -0600 @@ -31,7 +31,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: bellerophon.accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.ccode.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.ccode.xml Tue Dec 04 11:05:19 2012 -0600 @@ -64,7 +64,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: ccode.accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.check.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.check.xml Tue Dec 04 11:05:19 2012 -0600 @@ -64,7 +64,7 @@ <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.chimeras" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.perseus.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.perseus.xml Tue Dec 04 11:05:19 2012 -0600 @@ -34,7 +34,7 @@ <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.pintail.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.pintail.xml Tue Dec 04 11:05:19 2012 -0600 @@ -122,7 +122,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.slayer.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.slayer.xml Tue Dec 04 11:05:19 2012 -0600 @@ -98,7 +98,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: slayer.accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.uchime.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chimera.uchime.xml Tue Dec 04 11:05:19 2012 -0600 @@ -149,7 +149,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chop.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/chop.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -10,6 +10,7 @@ --keep=$keep $countgaps $short + --processors=8 </command> <inputs> <param name="fasta" type="data" format="fasta,align" label="fasta - Sequences to be chopped"/> @@ -26,7 +27,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/classify.otu.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/classify.otu.xml Tue Dec 04 11:05:19 2012 -0600 @@ -85,7 +85,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/classify.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/classify.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -121,7 +121,7 @@ <data format="tax.summary" name="tax_summary" label="${tool.name} on ${on_string}: tax.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/classify.tree.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/classify.tree.xml Tue Dec 04 11:05:19 2012 -0600 @@ -33,7 +33,7 @@ <data format_source="tabular" name="summary" label="${tool.name} on ${on_string}: taxonomy.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/clearcut.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/clearcut.xml Tue Dec 04 11:05:19 2012 -0600 @@ -64,7 +64,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.classic.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.classic.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ -<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.19.0"> +<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.27.0"> <description>Assign sequences to OTUs (Dotur implementation)</description> <command interpreter="python"> mothur_wrapper.py @@ -9,6 +9,9 @@ #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if #if len($method.__str__) > 0: --method=$method #end if @@ -24,6 +27,7 @@ <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <!-- ? conditional - to hide complexity --> <param name="method" type="select" label="method - Select a Clustering Method" help=""> <option value="furthest">Furthest neighbor</option> @@ -54,7 +58,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.fragments.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.fragments.xml Tue Dec 04 11:05:19 2012 -0600 @@ -29,7 +29,7 @@ <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.split.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.split.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ -<tool id="mothur_cluster_split" name="Cluster.split" version="1.22.0"> +<tool id="mothur_cluster_split" name="Cluster.split" version="1.27.0"> <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> <command interpreter="python"> mothur_wrapper.py @@ -32,6 +32,10 @@ --taxlevel=$splitby.taxlevel #end if --splitmethod=$splitby.splitmethod + $splitby.classic + #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count #end if #if len($method.__str__) > 0: --method=$method @@ -82,8 +86,10 @@ <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> <param name="taxlevel" type="integer" value="3" label="taxlevel - taxonomy level for split (default=3)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> + <param name="classic" type="boolean" checked="false" truevalue="--classic=true" falsevalue="" label="classic - Use cluster.classic" </when> </conditional> <!-- splitby --> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name="method" type="select" label="method - Select a Clustering Method" help=""> <option value="furthest">Furthest neighbor</option> <option value="nearest">Nearest neighbor</option> @@ -115,7 +121,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cluster.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ -<tool id="mothur_cluster" name="Cluster" version="1.19.0"> +<tool id="mothur_cluster" name="Cluster" version="1.27.0"> <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> <command interpreter="python"> mothur_wrapper.py @@ -14,6 +14,9 @@ --name=$matrix.name #end if #end if + #if $count.__str__ != "None" and len($count.__str__) > 0: + --count=$count + #end if $sim #if float($cutoff.__str__) > 0.0: --cutoff=$cutoff @@ -41,6 +44,7 @@ <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> </when> </conditional> + <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <!-- ? conditional - to hide complexity --> <param name="method" type="select" label="method - Select a Clustering Method" help=""> <option value="furthest">Furthest neighbor</option> @@ -72,7 +76,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/collect.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/collect.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -85,7 +85,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/collect.single.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/collect.single.xml Tue Dec 04 11:05:19 2012 -0600 @@ -79,7 +79,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/consensus.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/consensus.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -56,7 +56,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cooccurrence.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/cooccurrence.xml Tue Dec 04 11:05:19 2012 -0600 @@ -61,7 +61,7 @@ <data format="tabular" name="out_summary" label="${tool.name} on ${on_string}: cooccurence.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/corr.axes.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/corr.axes.xml Tue Dec 04 11:05:19 2012 -0600 @@ -65,7 +65,7 @@ <data format="axes" name="corr_axes" label="${tool.name} on ${on_string}: corr.axes"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/count.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/count.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -7,6 +7,8 @@ --outputdir='$logfile.extra_files_path' #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$group + #elif isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__): + --count=$group #else: --group=$group #end if @@ -21,7 +23,7 @@ #end if </command> <inputs> - <param name="group" type="data" format="groups,shared" label="group or shared - Group file for sequence count"/> + <param name="group" type="data" format="groups,shared,count_table" label="group, shared, or count_table - Group file for sequence count"/> <conditional name="groupnames"> <param name="source" type="select" label="Filter group names"> <option value="none">Report on All Groups</option> @@ -47,7 +49,7 @@ <data format="tabular" name="grp_count" label="${tool.name} on ${on_string}: group.count" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/count.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/count.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,5 +1,5 @@ <tool id="mothur_count_seqs" name="Count.seqs" version="1.20.0" > - <description>counts the number of sequences represented by the representative</description> + <description>(aka make.table) counts the number of sequences represented by the representative</description> <command interpreter="python"> mothur_wrapper.py --cmd='count.seqs' @@ -14,6 +14,7 @@ --groups='$grouping.groups' #end if #end if + $large </command> <inputs> <param name="name" type="data" format="names" label="name - Sequences Name reference"/> @@ -30,13 +31,14 @@ </when> <when value="no"/> </conditional> <!-- use_groups --> + <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Datasets are large and may not fit in RAM"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="tabular" name="seq_count" label="${tool.name} on ${on_string}: seq.count" /> + <data format="count_table" name="seq_count" label="${tool.name} on ${on_string}: count_table" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests> @@ -51,11 +53,12 @@ **Command Documenation** -The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file. If a group_ file is given, it will also provide the group count breakdown. +The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown. .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _count.seqs: http://www.mothur.org/wiki/Count.seqs +.. _count_table: http://www.mothur.org/wiki/Count_File </help> </tool>
--- a/mothur/tools/mothur/create.database.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/create.database.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ -<tool id="mothur_create_database" name="Create.database" version="1.25.0" > +<tool id="mothur_create_database" name="Create.database" version="1.27.0" > <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description> <command interpreter="python"> mothur_wrapper.py @@ -7,7 +7,11 @@ --outputdir='$logfile.extra_files_path' ## --datasetid='$logfile.id' --new_file_path='$__new_file_path__' ## --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary' - --list=$otu + #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): + --shared=$otu + #else + --list=$otu + #end if --repfasta=$repfasta --repname=$repname --contaxonomy=$contaxonomy @@ -19,7 +23,7 @@ #end if </command> <inputs> - <param name="otu" type="data" format="list" label="list - OTU List "/> + <param name="otu" type="data" format="list,shared" label="list or shared - OTU List of Shared"/> <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="fasta file output by get.oturep"/> <param name="repname" type="data" format="names" label="repname - rep.names" @@ -38,7 +42,7 @@ <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests> @@ -53,9 +57,10 @@ **Command Documenation** -The create.database_ command reads a list_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. +The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. .. _list: http://www.mothur.org/wiki/List_file +.. _shared: http://www.mothur.org/wiki/Shared_file .. _create.database: http://www.mothur.org/wiki/Create.database
--- a/mothur/tools/mothur/degap.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/degap.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -15,7 +15,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/deunique.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/deunique.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -17,7 +17,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/deunique.tree.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/deunique.tree.xml Tue Dec 04 11:05:19 2012 -0600 @@ -17,7 +17,7 @@ <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: deunique.tre" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/dist.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/dist.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -49,7 +49,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/dist.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/dist.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -118,7 +118,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/fastq.info.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/fastq.info.xml Tue Dec 04 11:05:19 2012 -0600 @@ -22,7 +22,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/filter.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/filter.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -57,7 +57,7 @@ <data format="align" name="out_fasta" label="${tool.name} on ${on_string}: filtered fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/get.coremicrobiome.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,82 @@ +<tool id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="1.26.0"> + <description>fraction of OTUs for samples or abundances</description> + <command interpreter="python"> + mothur_wrapper.py + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__, "'^\S+\.core\.microbiome$:'" + $core_microbiome.__str__] + --cmd='get.coremicrobiome' + --outputdir='$logfile.extra_files_path' + #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 + #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=$groups + #end if + #if len($abundance.__str__) > 0 or len($samples.__str__) > 0: + #if len($abundance.__str__) > 0: + --abundance=$abundance + #end if + #if len($samples.__str__) > 0: + --samples=$samples + #end if + #set results = $results + ["'^\S+\.core\.microbiomelist$:'" + $core_microbiomelist.__str__] + #end if + --result=#echo ','.join($results) + </command> + <inputs> + <param name="otu" type="data" format="shared,relabund" 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" /> + </options> + </param> + <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> + <options> + <filter type="data_meta" ref="otu" key="groups" /> + </options> + </param> + <param name="abundance" type="integer" optional="true" label="abundance - list OTU names at this abundance"> + <validator type="in_range" message="abundance is between 0 and 100" min="0" max="100"/> + </param> + <param name="samples" type="integer" optional="true" label="samples - minimum number of samples requied to list OTU names"> + <validator type="in_range" message="between 1 and number of samples in your file" min="1"/> + </param> + <param name="output" type="select" label="output - fraction or count"> + <option value="fraction" selected="true">fraction</option> + <option value="count">count</option> + </param> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="tabular" name="core_microbiome" label="${tool.name} on ${on_string}: core.microbiome"/> + <data format="tabular" name="core_microbiomelist" label="${tool.name} on ${on_string}: core.microbiomelist"> + <filter>(len(abundance.__str__) > 0 or len(samples.__str__) > 0)</filter> + </data> + </outputs> + <requirements> + <requirement type="package" version="1.27">mothur</requirement> + </requirements> + <tests> + </tests> + <help> +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances. + +.. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome + + + </help> +</tool>
--- a/mothur/tools/mothur/get.group.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.group.xml Tue Dec 04 11:05:19 2012 -0600 @@ -15,7 +15,7 @@ <data format="groups" name="bootgroups" label="${tool.name} on ${on_string}: bootGroups" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -94,7 +94,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.lineage.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.lineage.xml Tue Dec 04 11:05:19 2012 -0600 @@ -73,7 +73,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/get.otulabels.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,69 @@ +<tool id="mothur_get_otulabels" name="Get.otulabels" version="1.26.0"> + <description>Selects OTU labels</description> + <command interpreter="python"> + mothur_wrapper.py + #import re, os.path + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] + ## adds .pick before the last extension to the input file + --cmd='get.otulabels' + --outputdir='$logfile.extra_files_path' + --accnos=$accnos + #if $constaxonomy_in.__str__ != "None" and len($constaxonomy_in.__str__) > 0: + --constaxonomy=$constaxonomy_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy_in.__str__)) + ":'" + $constaxonomy_out.__str__] + #end if + #if $otucorr_in.__str__ != "None" and len($otucorr_in.__str__) > 0: + --otucorr=$otucorr_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($otucorr_in.__str__)) + ":'" + $otucorr_out.__str__] + #end if + #if $corraxes_in.__str__ != "None" and len($corraxes_in.__str__) > 0: + --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) + </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"/> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <!-- format should be set to match input --> + <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> + <filter>constaxonomy_in != None</filter> + </data> + <!-- format should be set to match input --> + <data format_source="otucorr_in" name="otucorr_out" label="${tool.name} on ${on_string}: pick.otu.corr"> + <filter>otucorr_in != None</filter> + </data> + <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> + <filter>constaxonomy_in != None</filter> + </data> + </outputs> + <requirements> + <requirement type="package" version="1.27">mothur</requirement> + </requirements> + <tests> + </tests> + <help> +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The get.otulabels_ command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. + +.. _classify.otu: http://www.mothur.org/wiki/Classify.otu +.. _corr.axes: http://www.mothur.org/wiki/Corr.axes +.. _otu.association: http://www.mothur.org/wiki/Otu.association +.. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels + + </help> +</tool>
--- a/mothur/tools/mothur/get.otulist.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.otulist.xml Tue Dec 04 11:05:19 2012 -0600 @@ -38,7 +38,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.oturep.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.oturep.xml Tue Dec 04 11:05:19 2012 -0600 @@ -90,7 +90,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.otus.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.otus.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.rabund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.rabund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -30,7 +30,7 @@ <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.relabund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.relabund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -42,7 +42,7 @@ <data format="relabund" name="relabund" label="${tool.name} on ${on_string}: relabund" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.sabund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.sabund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -27,7 +27,7 @@ <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -77,7 +77,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.sharedseqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/get.sharedseqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -78,7 +78,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/hcluster.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/hcluster.xml Tue Dec 04 11:05:19 2012 -0600 @@ -76,7 +76,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/heatmap.bin.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/heatmap.bin.xml Tue Dec 04 11:05:19 2012 -0600 @@ -102,7 +102,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/heatmap.sim.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/heatmap.sim.xml Tue Dec 04 11:05:19 2012 -0600 @@ -86,7 +86,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/homova.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/homova.xml Tue Dec 04 11:05:19 2012 -0600 @@ -26,7 +26,7 @@ <data format="tabular" name="homova" label="${tool.name} on ${on_string}: homova"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/indicator.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/indicator.xml Tue Dec 04 11:05:19 2012 -0600 @@ -51,7 +51,7 @@ <data format="tabular" name="summary" label="${tool.name} on ${on_string}: indicator.summary"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/libshuff.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/libshuff.xml Tue Dec 04 11:05:19 2012 -0600 @@ -52,7 +52,7 @@ <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/list.otulabels.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,66 @@ +<tool id="mothur_list_otulabels" name="List.otulabels" version="1.26.0"> + <description>Lists otu labels from shared or relabund file</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='list.otulabels' + --outputdir='$logfile.extra_files_path' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otulabels$:'$otulabels + #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 + #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=$groups + #end if + </command> + <inputs> + <param name="otu" type="data" format="shared,relabund" label="shared or relabund - OTU Shared or Relabund"/> + <param name="label" type="select" label="label - OTU Labels" multiple="true"> + <options> + <filter type="data_meta" ref="otu" key="labels" /> + </options> + </param> + <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> + <options> + <filter type="data_meta" ref="otu" key="groups" /> + </options> + </param> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="otulabels" name="otulabels" label="${tool.name} on ${on_string}: otulabels"/> + </outputs> + <requirements> + <requirement type="package" version="1.27">mothur</requirement> + </requirements> + <tests> + </tests> + <help> +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands. + +.. _list.otulabels: http://www.mothur.org/wiki/List.otulabels +.. _classify.otu: http://www.mothur.org/wiki/Classify.otu +.. _otu.association: http://www.mothur.org/wiki/Otu.association +.. _corr.axes: http://www.mothur.org/wiki/Corr.axes +.. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels +.. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels +.. _shared: http://www.mothur.org/wiki/Shared_file +.. _relabund: http://www.mothur.org/wiki/Get.relabund + + + </help> +</tool>
--- a/mothur/tools/mothur/list.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/list.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ <data format="accnos" name="out_file" label="${tool.name} on ${on_string}: accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.biom.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.biom.xml Tue Dec 04 11:05:19 2012 -0600 @@ -45,7 +45,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/make.contigs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,106 @@ +<tool id="mothur_make_contigs" name="Make.contigs" version="1.26.0"> + <description>Aligns paired forard and reverse fastq files to contigs as fasta and quality</description> + <command interpreter="python"> + mothur_wrapper.py + --cmd='make.contigs' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.contigs\.fasta$:'$fasta,'^\S+\.contigs\.qual$:'$qual,'^\S+\.contigs\.mismatch$:'$mismatch + --outputdir='$logfile.extra_files_path' + --ffastq=$ffastq + --rfastq=$rfastq + --align=$align + #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 + #end if + + #if $match.__str__ != '': + --match=$match + #end if + #if $mismatch.__str__ != '': + --mismatch=$mismatch + #end if + #if $gapopen.__str__ != '': + --gapopen=$gapopen + #end if + #if $gapextend.__str__ != '': + --gapextend=$gapextend + #end if + #if $threshold.__str__ != '': + --threshold=$threshold + #end if + --processors=8 + </command> + <inputs> + <param name="ffastq" type="data" format="fastq" label="ffastq - Forward Fastq Sequence file"/> + <param name="rfastq" type="data" format="fastq" label="rfastq - Reverse Fastq Sequence file"/> + <param name="align" type="select" label="align - Select a pairwise alignment method" help=""> + <option value="gotoh" selected="true">gotoh (default)</option> + <option value="needleman">needleman</option> + </param> + <conditional name="oligo"> + <param name="add" type="select" label="Trim with an oligos file?" help=""> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="oligos" type="data" format="oligos" optional="true" label="oligos - barcodes and primers" + 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. "/> + <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> + </when> + </conditional> + <param name="match" type="integer" value="1" optional="true" label="match - Pairwise alignment reward for a match"/> + <param name="mismatch" type="integer" value="-1" optional="true" label="mismatch - Pairwise alignment penalty for a mismatch"/> + <param name="gapopen" type="integer" value="-2" optional="true" label="gapopen - Pairwise alignment penalty for opening a gap"/> + <param name="gapextend" type="integer" value="-1" optional="true" label="gapextend - Pairwise alignment penalty for extending a gap"/> + <param name="threshold" type="integer" value="40" optional="true" label="threshold - for quality scores" + help="When we are merging the overlapping regions, in the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it."> + <validator type="in_range" message="threshold can't be negative" min="0"/> + </param> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="fasta" name="fasta" label="${tool.name} on ${on_string}: contigs.fasta"/> + <data format="qual" name="qual" label="${tool.name} on ${on_string}: contigs.qual"/> + <data format="txt" name="mismatch" label="${tool.name} on ${on_string}: contigs.mismatch"/> + </outputs> + <requirements> + <requirement type="package" version="1.27">mothur</requirement> + </requirements> + <tests> + </tests> + <help> +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files. + +.. _make.contigs: http://www.mothur.org/wiki/Make.contigs + + </help> +</tool>
--- a/mothur/tools/mothur/make.design.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.design.xml Tue Dec 04 11:05:19 2012 -0600 @@ -29,7 +29,7 @@ <data format="design" name="design" label="${tool.name} on ${on_string}: design" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.fastq.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.fastq.xml Tue Dec 04 11:05:19 2012 -0600 @@ -24,7 +24,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.group.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.group.xml Tue Dec 04 11:05:19 2012 -0600 @@ -21,7 +21,7 @@ <data format="groups" name="output" label="${tool.name} on ${on_string}: group" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -48,7 +48,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.shared_from_biom.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/make.shared_from_biom.xml Tue Dec 04 11:05:19 2012 -0600 @@ -31,7 +31,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/mantel.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/mantel.xml Tue Dec 04 11:05:19 2012 -0600 @@ -27,7 +27,7 @@ <data format="tabular" name="mantel" label="${tool.name} on ${on_string}: mantel"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/merge.files.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/merge.files.xml Tue Dec 04 11:05:19 2012 -0600 @@ -54,7 +54,7 @@ <data format="input" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/merge.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/merge.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -85,7 +85,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/metastats.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/metastats.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/mothur_wrapper.py Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/mothur_wrapper.py Tue Dec 04 11:05:19 2012 -0600 @@ -4,7 +4,7 @@ http://www.mothur.org/ Supports mothur version -mothur v.1.24.0 +mothur v.1.27.0 Class encapsulating Mothur galaxy tool. Expect each invocation to include: @@ -195,10 +195,10 @@ 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','method','cutoff','hard','precision','sim','showabund','timing']}) - cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','method','cutoff','hard','sim','precision']}) + 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','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']}) + 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['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']}) @@ -206,10 +206,10 @@ cmd_dict['cooccurrence'] = dict({'required' : ['shared'], 'optional' : ['iters','metric','matrixmodel','groups','label']}) cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) - cmd_dict['count.groups'] = dict({'required' : ['group','shared'], 'optional' : ['accnos','groups']}) - cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups']}) + 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, repfasta','repname','contaxonomy'], 'optional' : ['group','label']}) + cmd_dict['create.database'] = dict({'required' : [['list','shared'],'repfasta','repname','contaxonomy'], 'optional' : ['group','label']}) cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) @@ -238,6 +238,7 @@ 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['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) @@ -248,7 +249,7 @@ cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']}) - cmd_dict['otu.association'] = dict({'required' : [['shared','relabund']], 'optional' : ['groups', 'label','method']}) + 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']}) @@ -261,7 +262,7 @@ cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']}) 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']}) + cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble','design','sets','groupmode']}) 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']}) @@ -273,7 +274,7 @@ 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['shhh.flows'] = dict({'required' : [['flow','files']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','processors']}) + cmd_dict['shhh.flows'] = dict({'required' : [['flow','files']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','large','processors']}) cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','files']], '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']}) @@ -331,6 +332,8 @@ parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' ) parser.add_option( '--fasta', dest='fasta', help='fasta file paths' ) parser.add_option( '--fastq', dest='fastq', help='fastq file paths' ) + parser.add_option( '--ffastq', dest='ffastq', help='forward fastq file' ) + parser.add_option( '--rfastq', dest='rfastq', help='reverse fastq file' ) parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' ) parser.add_option( '--repfasta', dest='repfasta', help='fasta file paths' ) parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' ) @@ -401,6 +404,7 @@ parser.add_option( '--soft', dest='soft', type='int', help='Soft Mask - percentage required to retain column. (0-100)' ) parser.add_option( '--hard', dest='hard', help='Hard Column Filter - A file should only contain one line consisting of 0 and 1 chars' ) parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' ) + parser.add_option( '--count', dest='count', help='Count file' ) parser.add_option( '--countends', dest='countends', help='Penalize terminal gaps' ) parser.add_option( '--cutoff', dest='cutoff', help='Distance Cutoff threshold, discard larger distances' ) parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' ) @@ -515,6 +519,7 @@ parser.add_option( '--matrixtype', dest='matrixtype', help='' ) parser.add_option( '--consensus', dest='consensus', help='boolean' ) parser.add_option( '--biom', dest='biom', help='biom file' ) + parser.add_option( '--classic', dest='classic', help='boolean' ) # include read.otu options parser.add_option( '--rabund', dest='rabund', help='' ) parser.add_option( '--sabund', dest='sabund', help='' ) @@ -653,10 +658,21 @@ if re.match(pattern,line): chimera_count += 1 info += "Chimeras: %d" % chimera_count + elif options.cmd == 'count.groups': + fh = open(os.path.join(outputdir,'tmp.groups.count'),'w') + for line in tmp_stdout: + m = re.match('(.+) contains (\d+)\.',line) + if m and len(m.groups()) == 2: + info += line + print >> fh, "%s\t%s\n" % (m.group(1),m.group(2)) + fh.close() else: found_begin = False info_chars = 0 for line in tmp_stdout: + if re.match('mothur > ' + options.cmd + '\(.*\)', line): + found_begin = True + continue if line.find(outputdir) >= 0: continue if line.startswith('**************'): @@ -671,18 +687,19 @@ continue if re.match('.*\.\.\.\s*$',line): continue - if re.match('^\d*\s*$',line): + if re.match('^\d*\s*$',line) and not line.find(' contains '): continue # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands - if not options.cmd.startswith('unifrac') and re.match('^(unique|[0-9.]+)(\t\d+)*',line): # abundance from cluster commands, allow unique line into info + if (not (options.cmd.startswith('unifrac') or options.cmd.startswith('count.groups')) + and re.match('^(unique|[0-9.]+)(\t\d+)*',line)): # abundance from cluster commands, allow unique line into info continue if re.match('Output .*',line): break + if re.match('mothur > quit()',line): + break if found_begin and info_chars < 200: info += "%s" % line info_chars += len(line) - if re.match('mothur > ' + options.cmd + '\(.*\)', line): - found_begin = True tmp_stdout.close() print >> sys.stdout, info # Collect output files
--- a/mothur/tools/mothur/nmds.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/nmds.xml Tue Dec 04 11:05:19 2012 -0600 @@ -41,7 +41,7 @@ <data format="tabular" name="stress_nmds" label="${tool.name} on ${on_string}: nmds.stress"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/normalize.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/normalize.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -50,7 +50,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: norm.shared" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/otu.association.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/otu.association.xml Tue Dec 04 11:05:19 2012 -0600 @@ -21,6 +21,9 @@ #if $method.__str__ != "None" and len($method.__str__) > 0: --method=$method #end if + #if $metadata.__str__ != "None" and len($method.__str__) > 0: + --metadata=$metadata + #end if </command> <inputs> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> @@ -39,12 +42,13 @@ <option value="spearman">spearman</option> <option value="kendall">kendall</option> </param> + <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/otu.hierarchy.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/otu.hierarchy.xml Tue Dec 04 11:05:19 2012 -0600 @@ -33,7 +33,7 @@ <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pairwise.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pairwise.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -74,7 +74,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/parse.list.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/parse.list.xml Tue Dec 04 11:05:19 2012 -0600 @@ -27,7 +27,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/parsimony.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/parsimony.xml Tue Dec 04 11:05:19 2012 -0600 @@ -47,7 +47,7 @@ --> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pca.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pca.xml Tue Dec 04 11:05:19 2012 -0600 @@ -40,7 +40,7 @@ <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pcoa.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pcoa.xml Tue Dec 04 11:05:19 2012 -0600 @@ -18,7 +18,7 @@ <data format="tabular" name="loadings" label="${tool.name} on ${on_string}: loadings" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pcr.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pcr.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -99,7 +99,7 @@ </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/phylo.diversity.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/phylo.diversity.xml Tue Dec 04 11:05:19 2012 -0600 @@ -74,7 +74,7 @@ --> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/phylotype.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/phylotype.xml Tue Dec 04 11:05:19 2012 -0600 @@ -41,7 +41,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pre.cluster.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/pre.cluster.xml Tue Dec 04 11:05:19 2012 -0600 @@ -36,7 +36,7 @@ <data format="tabular" name="map_out" label="${tool.name} on ${on_string}: precluster.map" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/rarefaction.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ -<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.20.0"> +<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.26.0" force_history_refresh="True"> <description>Generate inter-sample rarefaction curves for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -12,6 +12,12 @@ #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' + #end if + #end if #if int($iters.__str__) > 0: --iters=$iters #end if @@ -19,6 +25,18 @@ #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if + #if $subsample.use.__str__ == 'yes': + #if $subsample.subsample.__str__ != '': + --subsample=$subsample.subsample + #else + --subsample=T + #end if + #if $subsample.subsampleiters.__str__ != '': + --subsampleiters=$subsample.subsampleiters + #end if + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.ave-std\.((unique|[0-9.]*)(\..*?)+\.shared\.rarefaction)$:tabular' + #end if </command> <inputs> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> @@ -31,22 +49,48 @@ <help>All groups will be analyzed by default if none are selected</help> <options> <filter type="data_meta" ref="otu" key="groups" /> + <!-- <filter type="add_value" name="all" value="all" /> + --> </options> </param> + <conditional name="design"> + <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" + help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> + <param name="sets" type="select" label="sets - group sets to analyze" multiple="true"> + <options> + <filter type="data_meta" ref="design" key="groups" /> + </options> + </param> + </when> + <when value="no"/> + </conditional> + <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/> <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option> <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option> </param> + <conditional name="subsample"> + <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample rarefactions"/> + <when value="yes"> + <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" + help="Leave blank to use the size of your smallest group"/> + <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/> + </when> + <when value="no"/> + </conditional> + </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/rarefaction.single.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.single.xml Tue Dec 04 11:05:19 2012 -0600 @@ -69,7 +69,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -94,7 +94,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.lineage.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.lineage.xml Tue Dec 04 11:05:19 2012 -0600 @@ -73,7 +73,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/remove.otulabels.xml Tue Dec 04 11:05:19 2012 -0600 @@ -0,0 +1,69 @@ +<tool id="mothur_remove_otulabels" name="Remove.otulabels" version="1.26.0"> + <description>Removes OTU labels</description> + <command interpreter="python"> + mothur_wrapper.py + #import re, os.path + #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] + ## adds .pick before the last extension to the input file + --cmd='remove.otulabels' + --outputdir='$logfile.extra_files_path' + --accnos=$accnos + #if $constaxonomy_in.__str__ != "None" and len($constaxonomy_in.__str__) > 0: + --constaxonomy=$constaxonomy_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy_in.__str__)) + ":'" + $constaxonomy_out.__str__] + #end if + #if $otucorr_in.__str__ != "None" and len($otucorr_in.__str__) > 0: + --otucorr=$otucorr_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($otucorr_in.__str__)) + ":'" + $otucorr_out.__str__] + #end if + #if $corraxes_in.__str__ != "None" and len($corraxes_in.__str__) > 0: + --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) + </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"/> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <!-- format should be set to match input --> + <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> + <filter>constaxonomy_in != None</filter> + </data> + <!-- format should be set to match input --> + <data format_source="otucorr_in" name="otucorr_out" label="${tool.name} on ${on_string}: pick.otu.corr"> + <filter>otucorr_in != None</filter> + </data> + <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> + <filter>constaxonomy_in != None</filter> + </data> + </outputs> + <requirements> + <requirement type="package" version="1.27">mothur</requirement> + </requirements> + <tests> + </tests> + <help> +**Mothur Overview** + +Mothur_, initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan, +provides bioinformatics for the microbial ecology community. + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The remove.otulabels_ command removes otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. + +.. _classify.otu: http://www.mothur.org/wiki/Classify.otu +.. _corr.axes: http://www.mothur.org/wiki/Corr.axes +.. _otu.association: http://www.mothur.org/wiki/Otu.association +.. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels + + </help> +</tool>
--- a/mothur/tools/mothur/remove.otus.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.otus.xml Tue Dec 04 11:05:19 2012 -0600 @@ -55,7 +55,7 @@ <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.rare.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.rare.xml Tue Dec 04 11:05:19 2012 -0600 @@ -91,7 +91,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/remove.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -77,7 +77,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/reverse.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/reverse.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -15,7 +15,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: rc.fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/screen.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/screen.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -101,7 +101,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sens.spec.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sens.spec.xml Tue Dec 04 11:05:19 2012 -0600 @@ -42,7 +42,7 @@ <data format="tabular" name="sensspec" label="${tool.name} on ${on_string}: sensspec" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/seq.error.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/seq.error.xml Tue Dec 04 11:05:19 2012 -0600 @@ -146,7 +146,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sffinfo.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sffinfo.xml Tue Dec 04 11:05:19 2012 -0600 @@ -53,7 +53,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/shhh.flows.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/shhh.flows.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ -<tool id="mothur_shhh_flows" name="Shhh.flows" version="1.22.0" force_history_refresh="True"> +<tool id="mothur_shhh_flows" name="Shhh.flows" version="1.26.0" force_history_refresh="True"> <description>Denoise flowgrams (PyroNoise algorithm)</description> <command interpreter="python"> mothur_wrapper.py @@ -23,6 +23,9 @@ #if $order.__str__.strip() != '': --order=$order #end if + #if $large.__str__ != '': + --large=$large + #end if --processors=8 </command> <inputs> @@ -69,6 +72,10 @@ <param name="order" type="text" value="" label="order - flow order for nucleotides in the sequencer" help="default is TACG"/> + + <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"/> + </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> @@ -79,7 +86,7 @@ <data format_source="tabular" name="shhh_counts" label="${tool.name} on ${on_string}: shhh.counts"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/shhh.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/shhh.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -32,7 +32,7 @@ <data format_source="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sort.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sort.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -69,7 +69,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/split.abund.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/split.abund.xml Tue Dec 04 11:05:19 2012 -0600 @@ -98,7 +98,7 @@ --> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/split.groups.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/split.groups.xml Tue Dec 04 11:05:19 2012 -0600 @@ -30,7 +30,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sub.sample.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/sub.sample.xml Tue Dec 04 11:05:19 2012 -0600 @@ -179,7 +179,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.qual.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.qual.xml Tue Dec 04 11:05:19 2012 -0600 @@ -20,7 +20,7 @@ <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -20,7 +20,7 @@ <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -1,4 +1,4 @@ -<tool id="mothur_summary_shared" name="Summary.shared" version="1.23.0" force_history_refresh="True"> +<tool id="mothur_summary_shared" name="Summary.shared" version="1.26.0" force_history_refresh="True"> <description>Summary of calculator values for OTUs</description> <command interpreter="python"> mothur_wrapper.py @@ -6,7 +6,6 @@ --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' --shared=$otu #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups @@ -19,6 +18,29 @@ #end if $all $distance + #if $subsample.use.__str__ == 'yes': + #if $subsample.subsample.__str__ != '': + --subsample=$subsample.subsample + #else + --subsample=T + #end if + #if $subsample.iters.__str__ != '': + --iters=$subsample.iters + #end if + #if len($subsample.output.__str__) > 0: + --output=$subsample.output + #end if + #if $subsample.as_datasets.__str__ == 'yes': + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + #if $subsample.output.__str__ == 'square': + ## patient70.fn.jest.0.16.lt.ave.dist + --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:square.dist' + #else + ## patient70.fn.jest.0.13.square.std.dist + --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:lower.dist' + #end if + #end if + #end if --processors=8 </command> <inputs> @@ -77,13 +99,29 @@ </param> <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/> <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Output a distance file for each calculator at each label"/> + + <conditional name="subsample"> + <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample distance matrices"/> + <when value="yes"> + <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" + help="Leave blank to use the size of your smallest group"/> + <param name="iters" type="integer" value="0" optional="true" label="iters - Number of times to run the subsample"/> + </when> + <when value="no"/> + <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> + <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option> + <option value="square">Phylip formatted Square Matrix</option> + </param> + <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each dataset" + help="the marices can be viewed from links in the logfile"/> + </conditional> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="summary" label="${tool.name} on ${on_string}: shared.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.single.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.single.xml Tue Dec 04 11:05:19 2012 -0600 @@ -8,7 +8,11 @@ --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+\.((\S+?)\.summary)$:tabular' #else: - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary + #if $subsample.use.__str__ == 'yes': + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups\.ave-std\.summary$:'$subsample_summary,'^\S+\.groups\.summary$:'$summary, + #else + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary + #end if #end if --outputdir='$logfile.extra_files_path' #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): @@ -33,6 +37,16 @@ #if int($size.__str__) > 0: --size=$size #end if + #if $subsample.use.__str__ == 'yes': + #if $subsample.subsample.__str__ != '': + --subsample=$subsample.subsample + #else + --subsample=T + #end if + #if $subsample.iters.__str__ != '': + --iters=$subsample.iters + #end if + #end if </command> <inputs> <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/> @@ -70,6 +84,15 @@ </param> <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/> <param name="size" type="integer" value="0" label="size - "/> + <conditional name="subsample"> + <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample distance matrices"/> + <when value="yes"> + <param name="subsample" type="integer" value="" optional="true" label="subsample - size of the sample" + help="If using shared input: may be left blank to use the size of your smallest group"/> + <param name="iters" type="integer" value="0" optional="true" label="iters - Number of times to run the subsample"/> + </when> + <when value="no"/> + </conditional> <param name="groupmode" type="boolean" truevalue="--groupmode=true" falsevalue="--groupmode=false" checked="true" label="groupmode - Collate shared summary results in one file" help="If false, create a summary file per group."/> @@ -79,9 +102,12 @@ <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary" > <filter>(otu.file_ext == 'shared' and groupmode == True)</filter> </data> + <data format="tabular" name="subsample_summary" label="${tool.name} on ${on_string}: ave-std.summary" > + <filter>(subsample['use'] and not (otu.file_ext == 'shared' and groupmode == False))</filter> + </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.tax.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/summary.tax.xml Tue Dec 04 11:05:19 2012 -0600 @@ -61,7 +61,7 @@ <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/tree.shared.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/tree.shared.xml Tue Dec 04 11:05:19 2012 -0600 @@ -136,7 +136,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/trim.flows.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/trim.flows.xml Tue Dec 04 11:05:19 2012 -0600 @@ -115,7 +115,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/trim.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/trim.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -151,7 +151,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unifrac.unweighted.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/unifrac.unweighted.xml Tue Dec 04 11:05:19 2012 -0600 @@ -110,7 +110,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unifrac.weighted.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/unifrac.weighted.xml Tue Dec 04 11:05:19 2012 -0600 @@ -117,7 +117,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unique.seqs.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/unique.seqs.xml Tue Dec 04 11:05:19 2012 -0600 @@ -20,7 +20,7 @@ <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/venn.xml Wed May 16 13:12:05 2012 -0500 +++ b/mothur/tools/mothur/venn.xml Tue Dec 04 11:05:19 2012 -0600 @@ -88,7 +88,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests>