-
Notifications
You must be signed in to change notification settings - Fork 4
/
tool_conf.xml
350 lines (349 loc) · 27.1 KB
/
tool_conf.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
<?xml version="1.0" ?>
<toolbox monitor="true">
<label id="5b97358a-94e5-44ca-bf28-312ad252b0a8" text="Tool Showcase"/>
<section id="0914476f-f380-4532-8dbf-fba110dee899" name="Commonly Used Tools">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/export.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gffFastaSplit.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/ncbi_entrez_eutils/efetch.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/mist3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/genome_map.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/genome_viz/linear_genome_plot.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk_viz/easyfig_cpt.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/phage_annotation_table.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_translate.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/feature_export.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_extract_sequence.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff2gb.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/cpt_gbkToGff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/interproscan-5.XX.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/lipory.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_makeblastdb.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_charges.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/genome_editor.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/phage_annotation_validator.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/shinefind.xml"/>
</section>
<label id="28dfd70e-db47-4b0c-b28d-ca3d63a53f14" text="Galaxy-Apollo Bridge"/>
<section id="f191ebcc-2443-4fd7-88a6-45a27167e0f3" name="Galaxy-Apollo Bridge">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/wig_rebase.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_prep_for_apollo.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/create_account.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/create_features_from_gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-4210/create_features_from_gff3.xml" label="new,experimental"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/create_or_update_organism.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/json2iframe.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/delete_features.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/delete_organism.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/shareOrg/share_with.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/list_organisms.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/list_organism_data.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/export.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gga-apollo/fetch_organism_jbrowse.xml"/>
</section>
<label id="494239c0-5e62-46ec-b9a0-39122963fbe1" text="Data Retreival"/>
<section id="fba2434e-1932-41d7-a632-f4b610ef21e0" name="Galaxy Tools">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/ncbi_entrez_eutils/efetch.xml"/>
</section>
<section id="0367a574-9504-44ea-abbf-6ea875f3362f" name="NCBI Entrez Utilities"/>
<section id="f3ebd36c-61d3-42ff-9657-6c84660a8c54" name="Get Data">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/wp_analysis/wp_data.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/refseq_analysis/refseq_confirm.xml"/>
</section>
<label id="32eb8fb3-532b-4d5d-8da8-a2e3c358cabe" text="Comparative Genomics and Visualization"/>
<section id="cb7b812b-0390-4ddb-928f-eedd367f0fd8" name="BCF Tools"/>
<section id="bcc5bb2c-3254-4011-95c8-cfc0a0e59e3f" name="CD-HIT">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/cdhit-reformat.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/cdhit-clustsize.xml"/>
</section>
<section id="67ca8f62-49a7-46dd-9631-88642824b085" name="CPT Circos Tools">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/PSM_Recombine.xml"/>
</section>
<section id="dc10c3dd-b25e-41c3-8f50-1c3ff311c317" name="Deeptools"/>
<section id="72a69e48-0bfc-45a0-bb51-e5ad36978a63" name="Genome comparison">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/prep/mist_prep.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/mist3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/diff.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_blastclust_fasta.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blastclust.xml"/>
</section>
<section id="7983abc5-c19f-495d-984c-d681aec1a360" name="Genome visualization">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/FlaGs/FlaGs.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/jbrowse/jbrowse-iuc/jbrowse.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/featuresvg.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/genome_map.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/genome_viz/linear_genome_plot.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk_viz/easyfig_cpt.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_color.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_snp_plot.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/phage_annotation_table.xml"/>
</section>
<section id="7de17161-4bd8-41ca-8838-2d0777b752a3" name="Multiple sequence alignment">
<label id="3f2511b5-1947-43ef-a081-d252b6855dbc" text="MAF Tools Suite"/>
</section>
<section id="91ab189f-f9ed-4de0-91e9-0a7b48666867" name="MUMmer Toolsuite"/>
<section id="8b74ad60-d551-401c-b9cf-a9a4b7c14cea" name="ProgressiveMauve">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/xmfa2gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/xmfa2bigwig.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/xmfa2tbl.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/cpt_mauve_graph.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/mauve.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blast2pxmfa.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/lcb_split.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/comparative/cluster_lcbs.xml"/>
</section>
<label id="68e2b686-330a-4130-8b6b-61712ceb09d1" text="File Manipulation"/>
<section id="092e6fcf-fb52-4006-b763-801e692ee8a8" name="Graph/Display Data"/>
<section id="005e6eb3-4a0a-48d8-b64f-a95341a41f88" name="Convert Common Formats">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_extract_sequence2.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff2gb.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/cpt_gbkToGff3.xml"/>
</section>
<section id="01e8428a-b64b-41d8-b315-ba7af523a33c" name="FASTA manipulation">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_bin.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_bin_post.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_concat.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_append.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_ligate.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_reopen.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_chop.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/util/cpt_mutate.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_split.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_revcom.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/ParDRe/pardre.xml"/>
<label id="26dff739-55ae-40a3-a450-2da1e8973be1" text="Header"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_ID_swapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_rename.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_rename_nodesc.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_remove_id.xml"/>
<label id="88ee6e39-1e37-47a1-94b1-7756284675b4" text="Filter / Extract"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_dedup.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_regex_search.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_translate.xml"/>
<label id="7bc01627-ebb1-4a58-be21-e2df02e5143e" text="Toolshed Tools"/>
</section>
<section id="97d06cb1-743c-47e3-8943-e6e8e4b80449" name="GenBank File Manipulation">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/remove_feature.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/remove_tag.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/renumber.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/revcom.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/split_gbks.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/correct_gene_model.xml"/>
<label id="be4a8e9f-6fc6-40cb-8bf5-3417ea7635fd" text="Filter / Extract"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/find_by_tag.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/split_on_qualifier.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/subsection.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/feature_export.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/seq_export.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/authorship.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/info_export.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/source.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/adjacent_features.xml"/>
</section>
<section id="37318502-d2e9-4ae9-9927-2a79309d245b" name="GFF3 Manipulation">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_reformat.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/fix_ncbi.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_validator.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_fix_sixpack.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_rebase.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_reopen.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_revcom.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_add_parents_to_cds.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_split_into_frames.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_remove_fasta_sequences.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/remove_annotations.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_table_annotations.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/retype_features.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/rebase_features.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_parent_child_map.xml"/>
<label id="88c5c36a-ed70-4b6b-bb54-3ad0d58a5f5d" text="Filter / Extract"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/filter_type.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_filter.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_location_filter.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_contains_location.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_require_phage_start.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_require_sd.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/extract_qualifiers.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_extract_introns.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_extract_sequence.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/webapollo/gffFastaSplit.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/intersect.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/intersect_and_adjacent.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/neighbours.xml"/>
</section>
<section id="41c70217-fbed-466c-87fe-ab0b9e55604b" name="BED manipulation"/>
<section id="d8b6e0f0-0906-43ea-8286-5a3dc5053d7a" name="Specialty File Format Conversion">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_splitgff.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/util/cpt_convert_glimmer_to_gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/util/cpt_convert_mga_to_gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/wigToBigWig.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/cpt_fixGbkConversion.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_fix_genemarks.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/util/tRNAscan_to_gff_SE_format.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/fix-aragorn-gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/lipoP_to_gff3.xml"/>
</section>
<section id="d2c6f286-ca8e-4328-baa0-f641ac153543" name="Text Manipulation">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/proximity/searchFile.xml"/>
<label id="3c9de5d3-d10e-48c7-9c86-1313b305b6c1" text="Filter and sort"/>
<label id="2e1c8715-47bb-4cef-a702-606472556d6d" text="Join, Subtract and Group"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/text/uniq.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/text/intersect.xml"/>
</section>
<label id="cc58c282-abd9-471d-9df1-384aae3ab6dc" text="Genome File Manipulation"/>
<section id="4d337048-5b08-4d1d-aac6-4364c03db486" name="Genome Polishing and Submission">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/add_tr.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/phage_renamer.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/rename.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/safe_reopen.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/genome_editor.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/autoreopen.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/sequin.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/gbk_to_five_col.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/five_col_to_gbk.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/cpt_validate_gbk.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/phage_annotation_validator.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/promote_qualifier.xml"/>
</section>
<label id="26fd327a-fb07-4e7f-98cb-0968ee1c851a" text="Structural Prediction"/>
<section id="53465ff2-7284-436c-b16c-8d5569c15cdb" name="ORF and Gene Prediction Tools">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/PHANOTATE/phanotate.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/get_orfs_or_cdss.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/shinefind.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/reading_garnier_output.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/gmsn.pl.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/tRNAscan-SE-2.0/trnaScan.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/transterm.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/rho.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/olgenie.xml"/>
</section>
<section id="a0d981ae-23a6-460b-a674-c79a790d7f48" name="Phage whole genome analyses">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/bacphlib.xml"/>
</section>
<label id="3c0a95bd-ad01-42f1-9475-41aefcd3b94d" text="Functional Prediction"/>
<section id="eff7f11c-09f1-4090-bf3c-dabbb6ce94e9" name="Domains and Signals">
<label id="0ff1e2c8-be52-4fd8-a164-2169a236ba3d" text="Protein"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/tmhmm.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/signalp.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/signalp6.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/interproscan-5.XX.xml"/>
<label id="0fbd2d78-ab6e-4807-80b2-41eba62bd28a" text="Nucleotide"/>
<label id="5d31897d-1b58-4968-ae16-370fd5cd4f8d" text="Motif Tools"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/bprom.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/bprom_gff3_converter.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/pattern_finder.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/motif_locator.xml"/>
</section>
<section id="8e11ff1b-8123-4b7d-bbe7-dccbd28b1057" name="HMMER"/>
<section id="654c0295-9456-4b10-b068-da0c692ecfd8" name="Lysis Gene Prediction">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/one-off/find_l_like_proteins.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/lipory.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/disruptin_finder.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/Disruptin_hydrophobicity_helicity_table_package.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/disruptin_proximity_2_lysis_genes.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/spanin/generate-putative-isp.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/spanin/generate-putative-osp.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/spanin/generate-putative-usp.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/spanin/findSpanin.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/SAR/SAR_finder.xml"/>
</section>
<section id="ec841d67-cc8b-4b57-9427-e7067e157ee6" name="NCBI BLAST+ 2.9">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast_latest/tools/ncbi_blast_plus/ncbi_makeblastdb.xml"/>
</section>
<section id="1642965e-e98d-4ddb-8fd1-768c3f0563bd" name="BLAST output processing">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/intron_detection.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/nuc_relate.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/prot_relate.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/list_taxids.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/split_blast.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blasttab_add_dice_column.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blasttab_dice_filter.xml"/>
<label id="747e727f-f93e-4011-bd50-44c76bfd3134" text="GFF3 Conversion"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blastxml_to_gapped_gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blastxml_to_gapped_gff3-nt.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blasttab_to_gapped_gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blastn_to_gff3.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blastp_to_gff3.xml"/>
</section>
<section id="e21682ca-670a-4cfc-aa60-fb727d4eaee9" name="Sequence Statistics">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/external/macrel.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_disambig.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_len.xml"/>
<label id="b07dfcaf-2830-4600-a950-3b41d6ecf8dc" text="Protein"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/helicalWheel/generateHelicalWheel.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_aastats.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_charges.xml"/>
<label id="f056ad55-701d-43fb-9812-8b139e1a36b6" text="Nucleotide"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/stop_stats.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/start_stats.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/start_stats.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/stop_stats.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_codonstats.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_proteininfo.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gff3/gff3_aa_stats.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/util/compare_codons.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/util/extract_ref_codons.xml"/>
</section>
<label id="1b62a5eb-51d5-4eed-8e62-5c493487b229" text="NGS read QC and manipulation"/>
<section id="a5886afb-23b2-48bd-9059-4297f1351e07" name="Read Manipulation"/>
<section id="0a1c2759-0a70-43a0-b41c-d68b1949bbcf" name="Nanopore Tools"/>
<section id="4b409a9a-b1a4-4ea3-833d-429112528828" name="Quality Control">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/abif/cpt_abif_info.xml"/>
</section>
<section id="9126b212-28ba-42be-b393-608652139e9d" name="seqtk"/>
<section id="0e2fb636-f61e-4516-8398-2da9f01f21be" name="Sequence Assembly">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/ngs/cpt_read_subset.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/ngs/contig_coverage.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/pause/pause_starts_to_wiggle.xml"/>
<label id="742553db-629e-471c-bede-e728b6f40d27" text="PacBio"/>
<label id="f2f7ffd7-a291-4f09-bb6b-49dce503dada" text="Read simulation"/>
<label id="7f7a3d27-98da-45be-b77b-590aadc756e8" text="SPAdes"/>
</section>
<label id="65645fe8-7bd2-4230-b50a-0e049302af5c" text="Read Mapping and Mutation Analysis"/>
<section id="6cc587c5-4de3-4f3f-b101-81edd038d5d4" name="DIAMOND"/>
<section id="8101b89a-bc7b-4e61-87ab-bc9d5cecb97c" name="Evolution"/>
<section id="96975045-67b2-40ef-a837-44ded922a779" name="Mutation Analysis">
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/virtual_suppressor_strain.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/one_snp/one_snp.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/fasta/fasta_codon_opt.xml"/>
</section>
<section id="461e4ca4-be8f-4393-8bed-003c18af0998" name="Picard Tools"/>
<section id="7e610619-a41d-4f31-aae3-0af0df1b1973" name="SAM Tools"/>
<section id="3b5b88ce-cea6-498b-abae-a9545040df7b" name="VarScan"/>
<section id="cf4e7982-82ce-4717-9b9f-86cd5d41dbaf" name="VCF Tools"/>
<section id="a5d1a2ba-4002-4179-9cb5-2cc8f0cffb96" name="Other read mapping tools"/>
<section id="00132cd5-41d6-40e7-ac5a-0c2e134018a0" name="Other variant calling tools">
<label id="ba6ccd88-ea00-490a-9b73-e25aa929a770" text="GATK"/>
<label id="a5bc5b73-32be-41b3-8854-9e85a352a169" text="Snippy"/>
</section>
<label id="c7225922-1c2f-4987-9902-0c6a9890fe14" text="Tool Packages"/>
<section id="047c3fd7-419a-4c2b-9ea3-c887403c775f" name="Bedtools"/>
<section id="06b98305-d174-4f7d-b3f0-535d5574e455" name="EMBOSS"/>
<section id="b2a5ce47-79b3-4d45-b506-627f1d4c46e0" name="Osiris"/>
<section id="a9256411-99de-44bc-90a4-43c14cd94dc1" name="ViennaRNA"/>
<label id="306f0d37-f0d1-4150-9ab9-05ab164436db" text="Deprecated"/>
<section id="33e81af1-4203-4a97-a659-87889316ad55" name="Comparative Genomics and Visualization">
<label id="5e627375-b511-499a-9709-da4eaf0e0fd2" text="Genome comparison"/>
<tool file="cpt2/galaxy-tools/tools/external/Prophet/Prophet.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/gbk/diff.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/prophageRelatedness.xml"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/phage/prophageToGFF.xml"/>
</section>
<section id="004a4a47-d24c-49bd-8650-98f2fd155e42" name="Functional Prediction">
<label id="bbe8ecf4-0973-475d-ada9-5eaaf2371c41" text="BLAST output processing"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/blast/blastxml_filter.xml"/>
<label id="ed7d914e-10bf-4869-b27f-546106273c59" text="Lysis Gene Prediction"/>
<label id="a28326e3-8695-4f08-9f30-e06278138a51" text="NCBI BLAST+"/>
<label id="5452ff3e-0802-4ddf-86aa-77d6fd49cfc2" text="Sequence Statistics"/>
<tool file="/galaxy/tools/cpt2/galaxy-tools/tools/one-off/starts-sds-scrubber.xml"/>
</section>
<section id="35cd65bd-c749-4ad0-9ef8-da1a95f17439" name="Deprecated">
<label id="a1c470c5-6df6-478b-a325-45b1d930df02" text="Soon to be Removed"/>
</section>
</toolbox>