Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/README @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
children | 040410b8167e |
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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) |