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comparison tools/tool_conf.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <?xml version="1.0"?>
2 <toolbox>
3 <label text="Sharp lab tools" id="sharplab" />
4 <section name="Single interval manipulation" id="singleinterval">
5 <tool file="mytools/bedclean.xml"/>
6 <tool file="mytools/bedsort.xml"/>
7 <tool file="mytools/collapseBed.xml" />
8 <tool file="mytools/makewindow.xml" />
9 <tool file="mytools/resize.xml" />
10 <tool file="mytools/random_interval.xml"/>
11 <tool file="mytools/shuffleBed.xml"/>
12 <tool file="mytools/genomeView.xml"/>
13 </section>
14 <section name="Meta-Analysis" id="xuebing">
15 <tool file="mytools/genomeView.xml"/>
16 <tool file="mytools/intersectbed.xml"/>
17 <tool file="mytools/closestBed.xml"/>
18 <tool file="mytools/spatial_proximity.xml"/>
19 <tool file="mytools/bwBinavg.xml"/>
20 <tool file="mytools/metaintv.xml" />
21 <tool file="mytools/metaintv_ext.xml" />
22 <tool file="mytools/alignr.xml" />
23 <tool file="mytools/align2multiple.xml" />
24 <tool file="mytools/align2database.xml" />
25 <tool file="mytools/intersectSig.xml" />
26 <tool file="mytools/bigWigAverageOverBed.xml" />
27 <tool file="mytools/endbias.xml" />
28 </section>
29 <section name="Statistics/Visualization" id="sharpvis">
30 <tool file="mytools/genomeView.xml"/>
31 <tool file="mytools/intervalSize.xml" />
32 <tool file="mytools/intersectSig.xml" />
33 <tool file="mytools/cdf.xml" />
34 <tool file="mytools/binaverage.xml" />
35 <tool file="mytools/alignvis.xml" />
36 <tool file="mytools/plotmatrix.xml" />
37 <tool file="mytools/venn.xml"/>
38 </section>
39 <section name="Text/Format manipulation" id="sharptext">
40 <tool file="mytools/collapseTab.xml" />
41 <tool file="mytools/fastqdump.xml" />
42 <tool file="mytools/bowtie2bed.xml" />
43 <tool file="mytools/sampline.xml" />
44 <tool file="mytools/headtail.xml" />
45 <tool file="mytools/convertEnsembl.xml" />
46 <tool file="mytools/removeDuplicate.xml" />
47 <tool file="mytools/bed_to_bam.xml" />
48 <tool file="mytools/makebigwig.xml" />
49
50 </section>
51 <section name="Sequence/Motif" id="sharpsequence">
52 <tool file="extract/extract_genomic_dna.xml" />
53 <tool file="mytools/revcompl.xml" />
54 <tool file="mytools/fastashuffle1.xml" />
55 <tool file="mytools/fastashuffle2.xml" />
56 <tool file="mytools/iupac2meme.xml" />
57 <tool file="mytools/seq2meme.xml" />
58 <tool file="mytools/memelogo.xml" />
59 <tool file="mytools/fastamarkov.xml" />
60 <tool file="mytools/meme.xml"/>
61 <tool file="mytools/dreme.xml"/>
62 <tool file="mytools/fimo2.xml"/>
63 <tool file="mytools/fimo2bed.xml"/>
64 <tool file="rgenetics/rgWebLogo3.xml" />
65 <tool file="mytools/splicesite.xml" />
66 </section>
67
68 <section name="Conservation/Other scores" id="score">
69 <tool file="mytools/phastCons.xml" />
70 </section>
71
72 <label text="selected tools" id="selectedtools" />
73 <section name="Get Data" id="sharpgetext">
74 <tool file="data_source/upload.xml"/>
75 <tool file="data_source/ucsc_tablebrowser.xml" />
76 <tool file="data_source/biomart.xml" />
77 </section>
78 <section name="Operate on Genomic Intervals" id="sharpbxops">
79 <tool file="new_operations/intersect.xml" />
80 <tool file="new_operations/subtract.xml" />
81 <tool file="new_operations/merge.xml" />
82 <tool file="new_operations/concat.xml" />
83
84 <tool file="mytools/closestBed.xml" />
85 <tool file="mytools/flankBed.xml" />
86 <tool file="mytools/shuffleBed.xml" />
87 <tool file="mytools/sortBed.xml" />
88
89 <tool file="new_operations/basecoverage.xml" />
90 <tool file="new_operations/coverage.xml" />
91 <tool file="new_operations/complement.xml" />
92 <tool file="new_operations/cluster.xml" id="cluster" />
93 <tool file="new_operations/join.xml" />
94 <tool file="new_operations/get_flanks.xml" />
95 <tool file="new_operations/flanking_features.xml" />
96 <tool file="annotation_profiler/annotation_profiler.xml" />
97 </section>
98 <section name="Unix Tools" id="unix_tools">
99 <tool file="unix_tools/awk_tool.xml" />
100 <tool file="unix_tools/sed_tool.xml" />
101 <tool file="unix_tools/grep_tool.xml" />
102 <tool file="unix_tools/sort_tool.xml" />
103 <tool file="unix_tools/uniq_tool.xml" />
104 <tool file="unix_tools/cut_tool.xml" />
105 <tool file="unix_tools/join_tool.xml" />
106 <tool file="unix_tools/word_list_grep.xml" />
107 <tool file="unix_tools/remove_ending.xml" />
108 <tool file="unix_tools/find_and_replace.xml" />
109 </section>
110 <section name="Lift-Over" id="liftOver">
111 <tool file="extract/liftOver_wrapper.xml" />
112 </section>
113 <section name="Text Manipulation" id="textutil">
114 <tool file="filters/fixedValueColumn.xml" />
115 <tool file="stats/column_maker.xml" />
116 <tool file="filters/catWrapper.xml" />
117 <tool file="filters/cutWrapper.xml" />
118 <tool file="filters/mergeCols.xml" />
119 <tool file="filters/convert_characters.xml" />
120 <tool file="filters/CreateInterval.xml" />
121 <tool file="filters/cutWrapper.xml" />
122 <tool file="filters/changeCase.xml" />
123 <tool file="filters/pasteWrapper.xml" />
124 <tool file="filters/remove_beginning.xml" />
125 <tool file="filters/randomlines.xml" />
126 <tool file="filters/headWrapper.xml" />
127 <tool file="filters/tailWrapper.xml" />
128 <tool file="filters/trimmer.xml" />
129 <tool file="filters/wc_gnu.xml" />
130 <tool file="stats/dna_filtering.xml" />
131 <tool file="new_operations/tables_arithmetic_operations.xml" />
132 </section>
133 <section name="Filter and Sort" id="filter">
134 <tool file="stats/filtering.xml" />
135 <tool file="filters/sorter.xml" />
136 <tool file="filters/grep.xml" />
137 <label text="GFF" id="gff" />
138 <tool file="filters/gff/extract_GFF_Features.xml" />
139 <tool file="filters/gff/gff_filter_by_attribute.xml" />
140 <tool file="filters/gff/gff_filter_by_feature_count.xml" />
141 <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
142 </section>
143 <section name="Join, Subtract and Group" id="group">
144 <tool file="filters/joiner.xml" />
145 <tool file="filters/compare.xml"/>
146 <tool file="new_operations/subtract_query.xml"/>
147 <tool file="stats/grouping.xml" />
148 <tool file="new_operations/column_join.xml" />
149 </section>
150 <section name="Convert Formats" id="convert">
151 <tool file="filters/axt_to_concat_fasta.xml" />
152 <tool file="filters/axt_to_fasta.xml" />
153 <tool file="filters/axt_to_lav.xml" />
154 <tool file="filters/bed2gff.xml" />
155 <tool file="fasta_tools/fasta_to_tabular.xml" />
156 <tool file="filters/gff2bed.xml" />
157 <tool file="filters/lav_to_bed.xml" />
158 <tool file="maf/maf_to_bed.xml" />
159 <tool file="maf/maf_to_interval.xml" />
160 <tool file="maf/maf_to_fasta.xml" />
161 <tool file="fasta_tools/tabular_to_fasta.xml" />
162 <tool file="fastq/fastq_to_fasta.xml" />
163 <tool file="filters/wiggle_to_simple.xml" />
164 <tool file="filters/sff_extractor.xml" />
165 <tool file="filters/gtf2bedgraph.xml" />
166 <tool file="filters/wig_to_bigwig.xml" />
167 <tool file="filters/bed_to_bigbed.xml" />
168 <tool file="samtools/sam_to_bam.xml" />
169 <tool file="samtools/bam_to_sam.xml" />
170 <tool file="mytools/bedToBam.xml" />
171 <tool file="mytools/bamToBed.xml" />
172 </section>
173
174
175
176 <section name="FASTA manipulation" id="fasta_manipulation">
177 <tool file="fasta_tools/fasta_compute_length.xml" />
178 <tool file="fasta_tools/fasta_filter_by_length.xml" />
179 <tool file="fasta_tools/fasta_concatenate_by_species.xml" />
180 <tool file="fasta_tools/fasta_to_tabular.xml" />
181 <tool file="fasta_tools/tabular_to_fasta.xml" />
182 <tool file="fastx_toolkit/fasta_formatter.xml" />
183 <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
184 <tool file="fastx_toolkit/fastx_collapser.xml" />
185 </section>
186 <section name="NGS: QC and manipulation" id="NGS_QC">
187 <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
188 <tool file="rgenetics/rgFastQC.xml" />
189 <label text="Illumina fastq" id="illumina" />
190 <tool file="fastq/fastq_groomer.xml" />
191 <tool file="fastq/fastq_paired_end_splitter.xml" />
192 <tool file="fastq/fastq_paired_end_joiner.xml" />
193 <tool file="fastq/fastq_stats.xml" />
194 <label text="Roche-454 data" id="454" />
195 <tool file="metag_tools/short_reads_figure_score.xml" />
196 <tool file="metag_tools/short_reads_trim_seq.xml" />
197 <tool file="fastq/fastq_combiner.xml" />
198 <label text="AB-SOLiD data" id="solid" />
199 <tool file="next_gen_conversion/solid2fastq.xml" />
200 <tool file="solid_tools/solid_qual_stats.xml" />
201 <tool file="solid_tools/solid_qual_boxplot.xml" />
202 <label text="Generic FASTQ manipulation" id="generic_fastq" />
203 <tool file="fastq/fastq_filter.xml" />
204 <tool file="fastq/fastq_trimmer.xml" />
205 <tool file="fastq/fastq_trimmer_by_quality.xml" />
206 <tool file="fastq/fastq_masker_by_quality.xml" />
207 <tool file="fastq/fastq_paired_end_interlacer.xml" />
208 <tool file="fastq/fastq_paired_end_deinterlacer.xml" />
209 <tool file="fastq/fastq_manipulation.xml" />
210 <tool file="fastq/fastq_to_fasta.xml" />
211 <tool file="fastq/fastq_to_tabular.xml" />
212 <tool file="fastq/tabular_to_fastq.xml" />
213 <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
214 <tool file="fastx_toolkit/fastq_quality_converter.xml" />
215 <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
216 <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
217 <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
218 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
219 <tool file="fastx_toolkit/fastq_quality_filter.xml" />
220 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
221 <tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
222 <tool file="fastx_toolkit/fastx_barcode_splitter.xml" />
223 <tool file="fastx_toolkit/fastx_clipper.xml" />
224 <tool file="fastx_toolkit/fastx_collapser.xml" />
225 <tool file="fastx_toolkit/fastx_renamer.xml" />
226 <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
227 <tool file="fastx_toolkit/fastx_trimmer.xml" />
228 </section>
229 <section name="NGS: Mapping" id="solexa_tools">
230 <tool file="sr_mapping/bowtie_wrapper.xml" />
231 </section>
232 <section name="NGS: SAM Tools" id="samtools">
233 <tool file="samtools/sam_bitwise_flag_filter.xml" />
234 <tool file="samtools/sam2interval.xml" />
235 <tool file="samtools/sam_merge.xml" />
236 <tool file="samtools/sam_pileup.xml" />
237 <tool file="samtools/pileup_parser.xml" />
238 <tool file="samtools/pileup_interval.xml" />
239 <tool file="samtools/samtools_flagstat.xml" />
240 </section>
241 <section name="Functional Enrichment" id="enrichment">
242 <tool file="human_genome_variation/linkToDavid.xml"/>
243 </section>
244
245 <label text="other galaxy tools" id="galaxy_tools"/>
246 <section name="Extract Features" id="features">
247 <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
248 </section>
249 <section name="Fetch Alignments" id="fetchAlign">
250 <tool file="maf/interval2maf_pairwise.xml" />
251 <tool file="maf/interval2maf.xml" />
252 <tool file="maf/maf_split_by_species.xml"/>
253 <tool file="maf/interval_maf_to_merged_fasta.xml" />
254 <tool file="maf/genebed_maf_to_fasta.xml"/>
255 <tool file="maf/maf_stats.xml"/>
256 <tool file="maf/maf_thread_for_species.xml"/>
257 <tool file="maf/maf_limit_to_species.xml"/>
258 <tool file="maf/maf_limit_size.xml"/>
259 <tool file="maf/maf_by_block_number.xml"/>
260 <tool file="maf/maf_reverse_complement.xml"/>
261 <tool file="maf/maf_filter.xml"/>
262 </section>
263 <section name="Get Genomic Scores" id="scores">
264 <tool file="stats/wiggle_to_simple.xml" />
265 <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
266 <tool file="extract/phastOdds/phastOdds_tool.xml" />
267 </section>
268 <section name="Operate on Genomic Intervals" id="bxops">
269 <tool file="new_operations/intersect.xml" />
270 <tool file="new_operations/subtract.xml" />
271 <tool file="new_operations/merge.xml" />
272 <tool file="new_operations/concat.xml" />
273 <tool file="new_operations/basecoverage.xml" />
274 <tool file="new_operations/coverage.xml" />
275 <tool file="new_operations/complement.xml" />
276 <tool file="new_operations/cluster.xml" id="cluster" />
277 <tool file="new_operations/join.xml" />
278 <tool file="new_operations/get_flanks.xml" />
279 <tool file="new_operations/flanking_features.xml" />
280 <tool file="annotation_profiler/annotation_profiler.xml" />
281 </section>
282 <section name="Statistics" id="stats">
283 <tool file="stats/gsummary.xml" />
284 <tool file="filters/uniq.xml" />
285 <tool file="stats/cor.xml" />
286 <tool file="stats/generate_matrix_for_pca_lda.xml" />
287 <tool file="stats/lda_analy.xml" />
288 <tool file="stats/plot_from_lda.xml" />
289 <tool file="regVariation/t_test_two_samples.xml" />
290 <tool file="regVariation/compute_q_values.xml" />
291 <label text="GFF" id="gff" />
292 <tool file="stats/count_gff_features.xml" />
293 </section>
294 <section name="Wavelet Analysis" id="dwt">
295 <tool file="discreteWavelet/execute_dwt_var_perFeature.xml" />
296 <!--
297 Keep this section/tools commented until all of the tools have functional tests
298 <tool file="discreteWavelet/execute_dwt_IvC_all.xml" />
299 <tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
300 <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
301 <tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
302 -->
303 </section>
304 <section name="Graph/Display Data" id="plots">
305 <tool file="plotting/histogram2.xml" />
306 <tool file="plotting/scatterplot.xml" />
307 <tool file="plotting/bar_chart.xml" />
308 <tool file="plotting/xy_plot.xml" />
309 <tool file="plotting/boxplot.xml" />
310 <tool file="visualization/GMAJ.xml" />
311 <tool file="visualization/LAJ.xml" />
312 <tool file="visualization/build_ucsc_custom_track.xml" />
313 <tool file="maf/vcf_to_maf_customtrack.xml" />
314 <tool file="mutation/visualize.xml" />
315 </section>
316 <section name="Regional Variation" id="regVar">
317 <tool file="regVariation/windowSplitter.xml" />
318 <tool file="regVariation/featureCounter.xml" />
319 <tool file="regVariation/quality_filter.xml" />
320 <tool file="regVariation/maf_cpg_filter.xml" />
321 <tool file="regVariation/getIndels_2way.xml" />
322 <tool file="regVariation/getIndels_3way.xml" />
323 <tool file="regVariation/getIndelRates_3way.xml" />
324 <tool file="regVariation/substitutions.xml" />
325 <tool file="regVariation/substitution_rates.xml" />
326 <tool file="regVariation/microsats_alignment_level.xml" />
327 <tool file="regVariation/microsats_mutability.xml" />
328 <tool file="regVariation/delete_overlapping_indels.xml" />
329 <tool file="regVariation/compute_motifs_frequency.xml" />
330 <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" />
331 <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
332 <tool file="regVariation/draw_stacked_barplots.xml" />
333 <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
334 <tool file="regVariation/microsatellite_birthdeath.xml" />
335 </section>
336 <section name="Multiple regression" id="multReg">
337 <tool file="regVariation/linear_regression.xml" />
338 <tool file="regVariation/best_regression_subsets.xml" />
339 <tool file="regVariation/rcve.xml" />
340 </section>
341 <section name="Multivariate Analysis" id="multVar">
342 <tool file="multivariate_stats/pca.xml" />
343 <tool file="multivariate_stats/cca.xml" />
344 <tool file="multivariate_stats/kpca.xml" />
345 <tool file="multivariate_stats/kcca.xml" />
346 </section>
347 <section name="Evolution" id="hyphy">
348 <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
349 <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
350 <tool file="hyphy/hyphy_dnds_wrapper.xml" />
351 <tool file="evolution/mutate_snp_codon.xml" />
352 <tool file="evolution/codingSnps.xml" />
353 <tool file="evolution/add_scores.xml" />
354 </section>
355 <section name="Multiple Alignments" id="clustal">
356 <tool file="rgenetics/rgClustalw.xml" />
357 </section>
358 <section name="Metagenomic analyses" id="tax_manipulation">
359 <tool file="taxonomy/gi2taxonomy.xml" />
360 <tool file="taxonomy/t2t_report.xml" />
361 <tool file="taxonomy/t2ps_wrapper.xml" />
362 <tool file="taxonomy/find_diag_hits.xml" />
363 <tool file="taxonomy/lca.xml" />
364 <tool file="taxonomy/poisson2test.xml" />
365 </section>
366 <section name="FASTA manipulation" id="fasta_manipulation">
367 <tool file="fasta_tools/fasta_compute_length.xml" />
368 <tool file="fasta_tools/fasta_filter_by_length.xml" />
369 <tool file="fasta_tools/fasta_concatenate_by_species.xml" />
370 <tool file="fasta_tools/fasta_to_tabular.xml" />
371 <tool file="fasta_tools/tabular_to_fasta.xml" />
372 <tool file="fastx_toolkit/fasta_formatter.xml" />
373 <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
374 <tool file="fastx_toolkit/fastx_collapser.xml" />
375 </section>
376 <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
377 <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
378 <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
379 <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
380 <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
381 <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
382 <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
383 </section>
384 <section name="NGS: QC and manipulation" id="NGS_QC">
385 <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
386 <tool file="rgenetics/rgFastQC.xml" />
387 <label text="Illumina fastq" id="illumina" />
388 <tool file="fastq/fastq_groomer.xml" />
389 <tool file="fastq/fastq_paired_end_splitter.xml" />
390 <tool file="fastq/fastq_paired_end_joiner.xml" />
391 <tool file="fastq/fastq_stats.xml" />
392 <label text="Roche-454 data" id="454" />
393 <tool file="metag_tools/short_reads_figure_score.xml" />
394 <tool file="metag_tools/short_reads_trim_seq.xml" />
395 <tool file="fastq/fastq_combiner.xml" />
396 <label text="AB-SOLiD data" id="solid" />
397 <tool file="next_gen_conversion/solid2fastq.xml" />
398 <tool file="solid_tools/solid_qual_stats.xml" />
399 <tool file="solid_tools/solid_qual_boxplot.xml" />
400 <label text="Generic FASTQ manipulation" id="generic_fastq" />
401 <tool file="fastq/fastq_filter.xml" />
402 <tool file="fastq/fastq_trimmer.xml" />
403 <tool file="fastq/fastq_trimmer_by_quality.xml" />
404 <tool file="fastq/fastq_masker_by_quality.xml" />
405 <tool file="fastq/fastq_paired_end_interlacer.xml" />
406 <tool file="fastq/fastq_paired_end_deinterlacer.xml" />
407 <tool file="fastq/fastq_manipulation.xml" />
408 <tool file="fastq/fastq_to_fasta.xml" />
409 <tool file="fastq/fastq_to_tabular.xml" />
410 <tool file="fastq/tabular_to_fastq.xml" />
411 <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
412 <tool file="fastx_toolkit/fastq_quality_converter.xml" />
413 <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
414 <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
415 <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
416 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
417 <tool file="fastx_toolkit/fastq_quality_filter.xml" />
418 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
419 <tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
420 <tool file="fastx_toolkit/fastx_barcode_splitter.xml" />
421 <tool file="fastx_toolkit/fastx_clipper.xml" />
422 <tool file="fastx_toolkit/fastx_collapser.xml" />
423 <tool file="fastx_toolkit/fastx_renamer.xml" />
424 <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
425 <tool file="fastx_toolkit/fastx_trimmer.xml" />
426 </section>
427 <section name="NGS: Picard (beta)" id="picard_beta">
428 <label text="QC/Metrics for sam/bam" id="qcsambam"/>
429 <tool file="picard/picard_BamIndexStats.xml" />
430 <tool file="picard/rgPicardASMetrics.xml" />
431 <tool file="picard/rgPicardGCBiasMetrics.xml" />
432 <tool file="picard/rgPicardLibComplexity.xml" />
433 <tool file="picard/rgPicardInsertSize.xml" />
434 <tool file="picard/rgPicardHsMetrics.xml" />
435 <label text="bam/sam Cleaning" id="picard-clean" />
436 <tool file="picard/picard_AddOrReplaceReadGroups.xml" />
437 <tool file="picard/picard_ReorderSam.xml" />
438 <tool file="picard/picard_ReplaceSamHeader.xml" />
439 <tool file="picard/rgPicardFixMate.xml" />
440 <tool file="picard/rgPicardMarkDups.xml" />
441 </section>
442 <!--
443 Keep this section commented until it includes tools that
444 will be hosted on test/main. The velvet wrappers have been
445 included in the distribution but will not be hosted on our
446 public servers for the current time.
447 <section name="NGS: Assembly" id="ngs_assembly">
448 <label text="Velvet" id="velvet"/>
449 <tool file="sr_assembly/velvetg.xml" />
450 <tool file="sr_assembly/velveth.xml" />
451 </section>
452 -->
453 <section name="NGS: Mapping" id="solexa_tools">
454 <tool file="sr_mapping/lastz_wrapper.xml" />
455 <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
456 <tool file="sr_mapping/bowtie_wrapper.xml" />
457 <tool file="sr_mapping/bowtie_color_wrapper.xml" />
458 <tool file="sr_mapping/bwa_wrapper.xml" />
459 <tool file="sr_mapping/bwa_color_wrapper.xml" />
460 <tool file="sr_mapping/bfast_wrapper.xml" />
461 <tool file="metag_tools/megablast_wrapper.xml" />
462 <tool file="metag_tools/megablast_xml_parser.xml" />
463 <tool file="sr_mapping/PerM.xml" />
464 <tool file="sr_mapping/srma_wrapper.xml" />
465 <tool file="sr_mapping/mosaik.xml"/>
466 </section>
467 <section name="NGS: Indel Analysis" id="indel_analysis">
468 <tool file="indels/sam_indel_filter.xml" />
469 <tool file="indels/indel_sam2interval.xml" />
470 <tool file="indels/indel_table.xml" />
471 <tool file="indels/indel_analysis.xml" />
472 </section>
473 <section name="NGS: RNA Analysis" id="ngs-rna-tools">
474 <label text="RNA-seq" id="rna_seq" />
475 <tool file="ngs_rna/tophat_wrapper.xml" />
476 <tool file="ngs_rna/tophat_color_wrapper.xml" />
477 <tool file="ngs_rna/cufflinks_wrapper.xml" />
478 <tool file="ngs_rna/cuffcompare_wrapper.xml" />
479 <tool file="ngs_rna/cuffdiff_wrapper.xml" />
480 <label text="De novo Assembly" id="de_novo_assembly "/>
481 <tool file="ngs_rna/trinity_all.xml" />
482 <label text="Filtering" id="filtering" />
483 <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
484 </section>
485 <section name="NGS: SAM Tools" id="samtools">
486 <tool file="samtools/sam_bitwise_flag_filter.xml" />
487 <tool file="samtools/sam2interval.xml" />
488 <tool file="samtools/sam_to_bam.xml" />
489 <tool file="samtools/bam_to_sam.xml" />
490 <tool file="samtools/sam_merge.xml" />
491 <tool file="samtools/sam_pileup.xml" />
492 <tool file="samtools/pileup_parser.xml" />
493 <tool file="samtools/pileup_interval.xml" />
494 <tool file="samtools/samtools_flagstat.xml" />
495 </section>
496 <section name="NGS: GATK Tools" id="gatk">
497 <label text="Realignment" id="gatk_realignment" />
498 <tool file="gatk/realigner_target_creator.xml" />
499 <tool file="gatk/indel_realigner.xml" />
500 <label text="Base Recalibration" id="gatk_recalibration" />
501 <tool file="gatk/count_covariates.xml" />
502 <tool file="gatk/table_recalibration.xml" />
503 <tool file="gatk/analyze_covariates.xml" />
504 <label text="Genotyping" id="gatk_genotyping" />
505 <tool file="gatk/unified_genotyper.xml" />
506 </section>
507 <section name="NGS: Peak Calling" id="peak_calling">
508 <tool file="peak_calling/macs_wrapper.xml" />
509 <tool file="peak_calling/sicer_wrapper.xml" />
510 <tool file="peak_calling/ccat_wrapper.xml" />
511 <tool file="genetrack/genetrack_indexer.xml" />
512 <tool file="genetrack/genetrack_peak_prediction.xml" />
513 </section>
514 <section name="NGS: Simulation" id="ngs-simulation">
515 <tool file="ngs_simulation/ngs_simulation.xml" />
516 </section>
517 <section name="SNP/WGA: Data; Filters" id="rgdat">
518 <label text="Data: Import and upload" id="rgimport" />
519 <tool file="data_source/upload.xml"/>
520 <tool file="data_source/access_libraries.xml" />
521 <label text="Data: Filter and Clean" id="rgfilter" />
522 <tool file="rgenetics/rgClean.xml"/>
523 <tool file="rgenetics/rgPedSub.xml"/>
524 <tool file="rgenetics/rgLDIndep.xml"/>
525 <label text="Simulate" id="rgsim" />
526 <tool file="rgenetics/rgfakePhe.xml"/>
527 <tool file="rgenetics/rgfakePed.xml"/>
528 </section>
529 <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
530 <label text="QC; Eigenstrat" id="rgvisual" />
531 <tool file="rgenetics/rgQC.xml"/>
532 <tool file="rgenetics/rgEigPCA.xml"/>
533 <label text="LD; Manhattan/QQ; GRR" id="rgld" />
534 <tool file="rgenetics/rgHaploView.xml"/>
535 <tool file="rgenetics/rgManQQ.xml"/>
536 <tool file="rgenetics/rgGRR.xml"/>
537 </section>
538 <section name="SNP/WGA: Statistical Models" id="rgmodel">
539 <tool file="rgenetics/rgCaCo.xml"/>
540 <tool file="rgenetics/rgTDT.xml"/>
541 <tool file="rgenetics/rgGLM.xml"/>
542 <tool file="rgenetics/rgManQQ.xml"/>
543 </section>
544 <section name="Human Genome Variation" id="hgv">
545 <tool file="evolution/codingSnps.xml" />
546 <tool file="evolution/add_scores.xml" />
547 <tool file="human_genome_variation/sift.xml" />
548 <tool file="human_genome_variation/linkToGProfile.xml" />
549 <tool file="human_genome_variation/linkToDavid.xml"/>
550 <tool file="human_genome_variation/ctd.xml" />
551 <tool file="human_genome_variation/funDo.xml" />
552 <tool file="human_genome_variation/snpFreq.xml" />
553 <tool file="human_genome_variation/ldtools.xml" />
554 <tool file="human_genome_variation/pass.xml" />
555 <tool file="human_genome_variation/gpass.xml" />
556 <tool file="human_genome_variation/beam.xml" />
557 <tool file="human_genome_variation/lps.xml" />
558 <tool file="human_genome_variation/hilbertvis.xml" />
559 <tool file="human_genome_variation/freebayes.xml" />
560 </section>
561 <section name="Genome Diversity" id="gd">
562 <tool file="genome_diversity/extract_primers.xml" />
563 <tool file="genome_diversity/select_snps.xml" />
564 <tool file="genome_diversity/select_restriction_enzymes.xml" />
565 <tool file="genome_diversity/extract_flanking_dna.xml" />
566 </section>
567 <section name="VCF Tools" id="vcf_tools">
568 <tool file="vcf_tools/intersect.xml" />
569 <tool file="vcf_tools/annotate.xml" />
570 <tool file="vcf_tools/filter.xml" />
571 <tool file="vcf_tools/extract.xml" />
572 </section>
573 <section name="PacBio/Illumina Assembly" id="hybrid">
574 <tool file="ilmn_pacbio/quake.xml"/>
575 <tool file="ilmn_pacbio/quake_pe.xml"/>
576 <tool file="ilmn_pacbio/soap_denovo.xml"/>
577 <!--
578 Uncomment this tool when we support the HDF5 format
579 <tool file="ilmn_pacbio/smrtpipe_filter.xml"/>
580 -->
581 <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/>
582 <tool file="ilmn_pacbio/assembly_stats.xml"/>
583 </section>
584 <!--
585 TODO: uncomment the following EMBOSS section whenever
586 moving to test, but comment it in .sample to eliminate
587 it from buildbot functional tests since these tools
588 rarely change.
589 -->
590 <!--
591 <section name="EMBOSS" id="EMBOSSLite">
592 <tool file="emboss_5/emboss_antigenic.xml" />
593 <tool file="emboss_5/emboss_backtranseq.xml" />
594 <tool file="emboss_5/emboss_banana.xml" />
595 <tool file="emboss_5/emboss_biosed.xml" />
596 <tool file="emboss_5/emboss_btwisted.xml" />
597 <tool file="emboss_5/emboss_cai_custom.xml" />
598 <tool file="emboss_5/emboss_cai.xml" />
599 <tool file="emboss_5/emboss_chaos.xml" />
600 <tool file="emboss_5/emboss_charge.xml" />
601 <tool file="emboss_5/emboss_checktrans.xml" />
602 <tool file="emboss_5/emboss_chips.xml" />
603 <tool file="emboss_5/emboss_cirdna.xml" />
604 <tool file="emboss_5/emboss_codcmp.xml" />
605 <tool file="emboss_5/emboss_coderet.xml" />
606 <tool file="emboss_5/emboss_compseq.xml" />
607 <tool file="emboss_5/emboss_cpgplot.xml" />
608 <tool file="emboss_5/emboss_cpgreport.xml" />
609 <tool file="emboss_5/emboss_cusp.xml" />
610 <tool file="emboss_5/emboss_cutseq.xml" />
611 <tool file="emboss_5/emboss_dan.xml" />
612 <tool file="emboss_5/emboss_degapseq.xml" />
613 <tool file="emboss_5/emboss_descseq.xml" />
614 <tool file="emboss_5/emboss_diffseq.xml" />
615 <tool file="emboss_5/emboss_digest.xml" />
616 <tool file="emboss_5/emboss_dotmatcher.xml" />
617 <tool file="emboss_5/emboss_dotpath.xml" />
618 <tool file="emboss_5/emboss_dottup.xml" />
619 <tool file="emboss_5/emboss_dreg.xml" />
620 <tool file="emboss_5/emboss_einverted.xml" />
621 <tool file="emboss_5/emboss_epestfind.xml" />
622 <tool file="emboss_5/emboss_equicktandem.xml" />
623 <tool file="emboss_5/emboss_est2genome.xml" />
624 <tool file="emboss_5/emboss_etandem.xml" />
625 <tool file="emboss_5/emboss_extractfeat.xml" />
626 <tool file="emboss_5/emboss_extractseq.xml" />
627 <tool file="emboss_5/emboss_freak.xml" />
628 <tool file="emboss_5/emboss_fuzznuc.xml" />
629 <tool file="emboss_5/emboss_fuzzpro.xml" />
630 <tool file="emboss_5/emboss_fuzztran.xml" />
631 <tool file="emboss_5/emboss_garnier.xml" />
632 <tool file="emboss_5/emboss_geecee.xml" />
633 <tool file="emboss_5/emboss_getorf.xml" />
634 <tool file="emboss_5/emboss_helixturnhelix.xml" />
635 <tool file="emboss_5/emboss_hmoment.xml" />
636 <tool file="emboss_5/emboss_iep.xml" />
637 <tool file="emboss_5/emboss_infoseq.xml" />
638 <tool file="emboss_5/emboss_isochore.xml" />
639 <tool file="emboss_5/emboss_lindna.xml" />
640 <tool file="emboss_5/emboss_marscan.xml" />
641 <tool file="emboss_5/emboss_maskfeat.xml" />
642 <tool file="emboss_5/emboss_maskseq.xml" />
643 <tool file="emboss_5/emboss_matcher.xml" />
644 <tool file="emboss_5/emboss_megamerger.xml" />
645 <tool file="emboss_5/emboss_merger.xml" />
646 <tool file="emboss_5/emboss_msbar.xml" />
647 <tool file="emboss_5/emboss_needle.xml" />
648 <tool file="emboss_5/emboss_newcpgreport.xml" />
649 <tool file="emboss_5/emboss_newcpgseek.xml" />
650 <tool file="emboss_5/emboss_newseq.xml" />
651 <tool file="emboss_5/emboss_noreturn.xml" />
652 <tool file="emboss_5/emboss_notseq.xml" />
653 <tool file="emboss_5/emboss_nthseq.xml" />
654 <tool file="emboss_5/emboss_octanol.xml" />
655 <tool file="emboss_5/emboss_oddcomp.xml" />
656 <tool file="emboss_5/emboss_palindrome.xml" />
657 <tool file="emboss_5/emboss_pasteseq.xml" />
658 <tool file="emboss_5/emboss_patmatdb.xml" />
659 <tool file="emboss_5/emboss_pepcoil.xml" />
660 <tool file="emboss_5/emboss_pepinfo.xml" />
661 <tool file="emboss_5/emboss_pepnet.xml" />
662 <tool file="emboss_5/emboss_pepstats.xml" />
663 <tool file="emboss_5/emboss_pepwheel.xml" />
664 <tool file="emboss_5/emboss_pepwindow.xml" />
665 <tool file="emboss_5/emboss_pepwindowall.xml" />
666 <tool file="emboss_5/emboss_plotcon.xml" />
667 <tool file="emboss_5/emboss_plotorf.xml" />
668 <tool file="emboss_5/emboss_polydot.xml" />
669 <tool file="emboss_5/emboss_preg.xml" />
670 <tool file="emboss_5/emboss_prettyplot.xml" />
671 <tool file="emboss_5/emboss_prettyseq.xml" />
672 <tool file="emboss_5/emboss_primersearch.xml" />
673 <tool file="emboss_5/emboss_revseq.xml" />
674 <tool file="emboss_5/emboss_seqmatchall.xml" />
675 <tool file="emboss_5/emboss_seqret.xml" />
676 <tool file="emboss_5/emboss_showfeat.xml" />
677 <tool file="emboss_5/emboss_shuffleseq.xml" />
678 <tool file="emboss_5/emboss_sigcleave.xml" />
679 <tool file="emboss_5/emboss_sirna.xml" />
680 <tool file="emboss_5/emboss_sixpack.xml" />
681 <tool file="emboss_5/emboss_skipseq.xml" />
682 <tool file="emboss_5/emboss_splitter.xml" />
683 <tool file="emboss_5/emboss_supermatcher.xml" />
684 <tool file="emboss_5/emboss_syco.xml" />
685 <tool file="emboss_5/emboss_tcode.xml" />
686 <tool file="emboss_5/emboss_textsearch.xml" />
687 <tool file="emboss_5/emboss_tmap.xml" />
688 <tool file="emboss_5/emboss_tranalign.xml" />
689 <tool file="emboss_5/emboss_transeq.xml" />
690 <tool file="emboss_5/emboss_trimest.xml" />
691 <tool file="emboss_5/emboss_trimseq.xml" />
692 <tool file="emboss_5/emboss_twofeat.xml" />
693 <tool file="emboss_5/emboss_union.xml" />
694 <tool file="emboss_5/emboss_vectorstrip.xml" />
695 <tool file="emboss_5/emboss_water.xml" />
696 <tool file="emboss_5/emboss_wobble.xml" />
697 <tool file="emboss_5/emboss_wordcount.xml" />
698 <tool file="emboss_5/emboss_wordmatch.xml" />
699 </section>
700 -->
701 </toolbox>