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comparison mothur/README @ 35:95d75b35e4d2

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Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author certain cat
date Fri, 31 Oct 2014 15:09:32 -0400
parents 49058b1f8d3f
children 040410b8167e
comparison
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34:1be61ceb20d7 35:95d75b35e4d2
1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page 1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page
2
2 3
3 Mothur should be able to be auto-installed as a tool_dependency 4 Mothur should be able to be auto-installed as a tool_dependency
4 You may want to reorganize the tool panel after installing 5 You may want to reorganize the tool panel after installing
5 See below: Reorganize integrated_tool_panel.xml 6 See below: Reorganize integrated_tool_panel.xml
6 This was based on: http://www.mothur.org/wiki/Mothur_manual 7 This was based on: http://www.mothur.org/wiki/Mothur_manual
7 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used for mothur commands) 8 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used for mothur commands)
8 This will be set in: tool_dependencies/mothur/1.27/jjohnson/mothur_toolsuite/*/env.sh 9 This will be set in: tool_dependencies/mothur/1.27/jjohnson/mothur_toolsuite/*/env.sh
10 Requirements for auto installation:
11 - make (sudo-apt get install make)
12 - g++ (sudo apt-get install g++)
13 - gfortran (sudo apt-get install gfortran)
14 - pip (sudo apt-get install python-pip)
15 - simplejson (pip install simplejson)
16
17 Repository Dependency:
18 - BLAST Legacy ver. 2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/)
19 - The repository name should be package_blast_2_2_26 so it matches with the tool dependency.
20
9 21
10 Manual installation for Mothur: 22 Manual installation for Mothur:
11 Install mothur v.1.27 on your galaxy system so galaxy can execute the mothur command 23 Install mothur v.1.33 on your galaxy system so galaxy can execute the mothur command
12 ( This version of wrappers is designed for Mothur version 1.27 - it may work on later versions ) 24 ( This version of wrappers is designed for Mothur version 1.33- it may work on later versions )
13 http://www.mothur.org/wiki/Download_mothur 25 http://www.mothur.org/wiki/Download_mothur
14 http://www.mothur.org/wiki/Installation 26 http://www.mothur.org/wiki/Installation
15 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) 27 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
16 28
17 TreeVector is also packaged with this Mothur package to view phylogenetic trees: 29 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
124 import metagenomics # added for metagenomics mothur 136 import metagenomics # added for metagenomics mothur
125 137
126 138
127 139
128 add datatypes to: datatypes_conf.xml 140 add datatypes to: datatypes_conf.xml
129 <!-- Start Mothur Datatypes -->
130 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
131 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
132 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
133 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
134 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
135 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
136 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
137 <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
138 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
139 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
140 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
141 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
142 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
143 <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/>
144 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
145 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
146 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
147 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
148 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
149 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
150 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
151 <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
152 <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
153 </datatype>
154 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
155 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
156 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
157 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
158 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
159 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
160 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
161 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
162 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
163 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
164 <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
165 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
166 <!-- End Mothur Datatypes -->
167
168 Reorganize integrated_tool_panel.xml :
169 <section id="metagenomics_mothur" name="Metagenomics Mothur" version="">
170 <label text="Mothur Utilities" id="mothur_utilities"/>
171 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_files/1.19.0" />
172 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_files/1.19.0" />
173 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_groups/1.24.0" />
174 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_groups/1.24.0" />
175 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_groups/1.24.0" />
176 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_groups/1.22.0" />
177 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_design/1.19.0" />
178 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sub_sample/1.22.0" />
179 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sort_seqs/1.24.0" />
180 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_create_database/1.27.0" />
181 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/CONVERTER_ref_to_seq_taxomony/1.0.0" />
182 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
183 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sffinfo/1.24.0" />
184 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_flows/1.26.0" />
185 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_flows/1.22.0" />
186 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_seqs/1.23.0" />
187 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_contigs/1.26.0" />
188 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_fastq/1.19.0" />
189 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_fastq_info/1.24.0" />
190 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_seqs/1.19.0" />
191 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_qual/1.23.0" />
192 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_seqs/1.20.0" />
193 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_reverse_seqs/1.19.0" />
194 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_seqs/1.19.0" />
195 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_seqs/1.20.0" />
196 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_seqs/1.20.0" />
197 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcr_seqs/1.25.0" />
198 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_seqs/1.24.0" />
199 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unique_seqs/1.20.0" />
200 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_seqs/1.20.0" />
201 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chop_seqs/1.19.0" />
202 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_screen_seqs/1.23.0" />
203 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_filter_seqs/1.19.0" />
204 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_degap_seqs/1.20.0" />
205 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_consensus_seqs/1.20.0" />
206 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_seqs/1.19.0" />
207 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_check/1.19.0" />
208 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_seqs/1.19.0" />
209 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pairwise_seqs/1.19.0" />
210 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_abund/1.20.0" />
211 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_groups/1.20.0" />
212 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcoa/1.19.0" />
213 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pca/1.20.0" />
214 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_nmds/1.19.0" />
215 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_corr_axes/1.20.0" />
216 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_seqs/1.21.0" />
217 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_seq_error/1.22.0" />
218 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
219 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_bellerophon/1.20.0" />
220 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_ccode/1.20.0" />
221 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_check/1.20.0" />
222 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_perseus/1.23.0" />
223 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_pintail/1.20.0" />
224 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_slayer/1.22.0" />
225 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_uchime/1.22.0" />
226 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
227 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pre_cluster/1.23.0" />
228 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_fragments/1.20.0" />
229 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster/1.27.0" />
230 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_hcluster/1.19.0" />
231 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_classic/1.27.0" />
232 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_split/1.27.0" />
233 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_metastats/1.20.0" />
234 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sens_spec/1.19.0" />
235 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_otu/1.20.0" />
236 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parse_list/1.19.0" />
237 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otus/1.19.0" />
238 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otus/1.19.0" />
239 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_rare/1.20.0" />
240 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulist/1.19.0" />
241 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_oturep/1.23.0" />
242 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_otulabels/1.26.0" />
243 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulabels/1.26.0" />
244 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otulabels/1.26.0" />
245 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_hierarchy/1.19.0" />
246 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_rabund/1.19.0" />
247 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sabund/1.19.0" />
248 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_relabund/1.20.0" />
249 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared/1.22.0" />
250 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared_from_biom/1.25.0" />
251 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_biom/1.25.0" />
252 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_group/1.19.0" />
253 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_bin_seqs/1.20.0" />
254 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sharedseqs/1.20.0" />
255 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_tax/1.22.0" />
256 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
257 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_single/1.20.0" />
258 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_single/1.20.0" />
259 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_single/1.19.0" />
260 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_bin/1.20.0" />
261 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
262 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_shared/1.23.0" />
263 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_shared/1.26.0" />
264 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_normalize_shared/1.20.0" />
265 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_shared/1.26.0" />
266 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_association/1.24.0" />
267 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_shared/1.25.0" />
268 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_sim/1.23.0" />
269 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_venn/1.23.0" />
270 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_tree_shared/1.25.0" />
271 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_coremicrobiome/1.26.0" />
272 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
273 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parsimony/1.19.0" />
274 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_weighted/1.25.0" />
275 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_unweighted/1.25.0" />
276 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_libshuff/1.19.0" />
277 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_amova/1.19.0" />
278 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_homova/1.19.0" />
279 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_mantel/1.19.0" />
280 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_anosim/1.19.0" />
281 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cooccurrence/1.25.0" />
282 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
283 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_lineage/1.20.0" />
284 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_lineage/1.20.0" />
285 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylotype/1.19.0" />
286 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylo_diversity/1.20.0" />
287 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_clearcut/1.19.0" />
288 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_indicator/1.21.0" />
289 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_tree/1.20.0" />
290 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_tree/1.24.0" />
291 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/tree_vector/1.0" />
292 </section>
293
294
295 141
296 add mothur tools to: tool_conf.xml 142 add mothur tools to: tool_conf.xml
297 <section name="Metagenomics Mothur" id="metagenomics_mothur">
298 <label text="Mothur Utilities" id="mothur_utilities"/>
299 <tool file="mothur/merge.files.xml"/>
300 <tool file="mothur/make.group.xml"/>
301 <tool file="mothur/get.groups.xml"/>
302 <tool file="mothur/remove.groups.xml"/>
303 <tool file="mothur/merge.groups.xml"/>
304 <tool file="mothur/count.groups.xml"/>
305 <tool file="mothur/make.design.xml"/>
306 <tool file="mothur/sub.sample.xml"/>
307 <tool file="mothur/sort.seqs.xml"/>
308 <tool file="mothur/create.database.xml"/>
309 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
310 <tool file="mothur/sffinfo.xml"/>
311 <tool file="mothur/trim.flows.xml"/>
312 <tool file="mothur/shhh.flows.xml"/>
313 <tool file="mothur/shhh.seqs.xml"/>
314 <tool file="mothur/make.fastq.xml"/>
315 <tool file="mothur/fastq.info.xml"/>
316 <tool file="mothur/summary.seqs.xml"/>
317 <tool file="mothur/summary.qual.xml"/>
318 <tool file="mothur/count.seqs.xml"/>
319 <tool file="mothur/reverse.seqs.xml"/>
320 <tool file="mothur/list.seqs.xml"/>
321 <tool file="mothur/get.seqs.xml"/>
322 <tool file="mothur/remove.seqs.xml"/>
323 <tool file="mothur/trim.seqs.xml"/>
324 <tool file="mothur/pcr.seqs.xml"/>
325 <tool file="mothur/unique.seqs.xml"/>
326 <tool file="mothur/deunique.seqs.xml"/>
327 <tool file="mothur/chop.seqs.xml"/>
328 <tool file="mothur/screen.seqs.xml"/>
329 <tool file="mothur/filter.seqs.xml"/>
330 <tool file="mothur/degap.seqs.xml"/>
331 <tool file="mothur/consensus.seqs.xml"/>
332 <tool file="mothur/align.seqs.xml"/>
333 <tool file="mothur/align.check.xml"/>
334 <tool file="mothur/dist.seqs.xml"/>
335 <tool file="mothur/pairwise.seqs.xml"/>
336 <tool file="mothur/split.abund.xml"/>
337 <tool file="mothur/split.groups.xml"/>
338 <tool file="mothur/pcoa.xml"/>
339 <tool file="mothur/pca.xml"/>
340 <tool file="mothur/nmds.xml"/>
341 <tool file="mothur/corr.axes.xml"/>
342 <tool file="mothur/classify.seqs.xml"/>
343 <tool file="mothur/seq.error.xml"/>
344 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
345 <tool file="mothur/chimera.bellerophon.xml"/>
346 <tool file="mothur/chimera.ccode.xml"/>
347 <tool file="mothur/chimera.check.xml"/>
348 <tool file="mothur/chimera.perseus.xml"/>
349 <tool file="mothur/chimera.pintail.xml"/>
350 <tool file="mothur/chimera.slayer.xml"/>
351 <tool file="mothur/chimera.uchime.xml"/>
352 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
353 <tool file="mothur/pre.cluster.xml"/>
354 <tool file="mothur/cluster.fragments.xml"/>
355 <tool file="mothur/cluster.xml"/>
356 <tool file="mothur/hcluster.xml"/>
357 <tool file="mothur/cluster.classic.xml"/>
358 <tool file="mothur/cluster.split.xml"/>
359 <tool file="mothur/metastats.xml"/>
360 <tool file="mothur/sens.spec.xml"/>
361 <tool file="mothur/classify.otu.xml"/>
362 <tool file="mothur/parse.list.xml"/>
363 <tool file="mothur/get.otus.xml"/>
364 <tool file="mothur/remove.otus.xml"/>
365 <tool file="mothur/remove.rare.xml"/>
366 <tool file="mothur/get.otulist.xml"/>
367 <tool file="mothur/get.oturep.xml"/>
368 <tool file="mothur/otu.hierarchy.xml"/>
369 <tool file="mothur/get.rabund.xml"/>
370 <tool file="mothur/get.sabund.xml"/>
371 <tool file="mothur/get.relabund.xml"/>
372 <tool file="mothur/make.shared.xml"/>
373 <tool file="mothur/make.shared_from_biom.xml"/>
374 <tool file="mothur/make.biom.xml"/>
375 <tool file="mothur/get.group.xml"/>
376 <tool file="mothur/bin.seqs.xml"/>
377 <tool file="mothur/get.sharedseqs.xml"/>
378 <tool file="mothur/summary.tax.xml"/>
379 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
380 <tool file="mothur/collect.single.xml"/>
381 <tool file="mothur/rarefaction.single.xml"/>
382 <tool file="mothur/summary.single.xml"/>
383 <tool file="mothur/heatmap.bin.xml"/>
384 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
385 <tool file="mothur/collect.shared.xml"/>
386 <tool file="mothur/rarefaction.shared.xml"/>
387 <tool file="mothur/normalize.shared.xml"/>
388 <tool file="mothur/summary.shared.xml"/>
389 <tool file="mothur/otu.association.xml"/>
390 <tool file="mothur/dist.shared.xml"/>
391 <tool file="mothur/heatmap.sim.xml"/>
392 <tool file="mothur/venn.xml"/>
393 <tool file="mothur/tree.shared.xml"/>
394 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
395 <tool file="mothur/parsimony.xml"/>
396 <tool file="mothur/unifrac.weighted.xml"/>
397 <tool file="mothur/unifrac.unweighted.xml"/>
398 <tool file="mothur/libshuff.xml"/>
399 <tool file="mothur/amova.xml"/>
400 <tool file="mothur/homova.xml"/>
401 <tool file="mothur/mantel.xml"/>
402 <tool file="mothur/anosim.xml"/>
403 <tool file="mothur/cooccurrence.xml"/>
404 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
405 <tool file="mothur/get.lineage.xml"/>
406 <tool file="mothur/remove.lineage.xml"/>
407 <tool file="mothur/phylotype.xml"/>
408 <tool file="mothur/phylo.diversity.xml"/>
409 <tool file="mothur/clearcut.xml"/>
410 <tool file="mothur/indicator.xml"/>
411 <tool file="mothur/deunique.tree.xml"/>
412 <tool file="mothur/classify.tree.xml"/>
413 <tool file="mothur/TreeVector.xml"/>
414 </section> <!-- metagenomics_mothur -->
415 143
416 ############ DESIGN NOTES ######################################################################################################### 144 ############ DESIGN NOTES #########################################################################################################
417 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py 145 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
418 146
419 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands) 147 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)