diff mothur/README @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

--- 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"/>