forked from jmchilton/galaxy-central
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtool_conf.xml.main
234 lines (227 loc) · 10.2 KB
/
tool_conf.xml.main
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
<?xml version='1.0' encoding='utf-8'?>
<toolbox>
<section id="getext" name="Get Data">
<tool file="data_source/upload.xml" />
<tool file="data_source/ucsc_tablebrowser.xml" />
<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
<tool file="data_source/ebi_sra.xml" />
<tool file="data_source/biomart.xml" />
<tool file="data_source/gramene_mart.xml" />
<tool file="data_source/fly_modencode.xml" />
<tool file="data_source/worm_modencode.xml" />
<tool file="data_source/wormbase.xml" />
<tool file="data_source/eupathdb.xml" />
<tool file="genomespace/genomespace_file_browser_prod.xml" />
<tool file="genomespace/genomespace_importer.xml" />
</section>
<section id="send" name="Send Data">
<tool file="genomespace/genomespace_exporter.xml" />
</section>
<section id="liftOver" name="Lift-Over">
<tool file="extract/liftOver_wrapper.xml" />
</section>
<section id="textutil" name="Text Manipulation">
<tool file="filters/fixedValueColumn.xml" />
<tool file="stats/column_maker.xml" />
<tool file="filters/catWrapper.xml" />
<tool file="filters/condense_characters.xml" />
<tool file="filters/convert_characters.xml" />
<tool file="filters/mergeCols.xml" />
<tool file="filters/CreateInterval.xml" />
<tool file="filters/cutWrapper.xml" />
<tool file="filters/changeCase.xml" />
<tool file="filters/pasteWrapper.xml" />
<tool file="filters/remove_beginning.xml" />
<tool file="filters/randomlines.xml" />
<tool file="filters/headWrapper.xml" />
<tool file="filters/tailWrapper.xml" />
<tool file="filters/trimmer.xml" />
<tool file="filters/wc_gnu.xml" />
<tool file="filters/secure_hash_message_digest.xml" />
</section>
<section id="convert" name="Convert Formats">
<tool file="filters/bed2gff.xml" />
<tool file="fasta_tools/fasta_to_tabular.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="maf/maf_to_bed.xml" />
<tool file="maf/maf_to_interval.xml" />
<tool file="maf/maf_to_fasta.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
<tool file="filters/sff_extractor.xml" />
<tool file="filters/wig_to_bigwig.xml" />
<tool file="filters/bed_to_bigbed.xml" />
</section>
<section id="fasta_manipulation" name="FASTA manipulation">
<tool file="fasta_tools/fasta_compute_length.xml" />
<tool file="fasta_tools/fasta_filter_by_length.xml" />
<tool file="fasta_tools/fasta_concatenate_by_species.xml" />
<tool file="fasta_tools/fasta_to_tabular.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
</section>
<section id="filter" name="Filter and Sort">
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.xml" />
<tool file="stats/dna_filtering.xml" />
<label id="gff" text="GFF" />
<tool file="filters/gff/extract_GFF_Features.xml" />
<tool file="filters/gff/gff_filter_by_attribute.xml" />
<tool file="filters/gff/gff_filter_by_feature_count.xml" />
<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
</section>
<section id="group" name="Join, Subtract and Group">
<tool file="filters/joiner.xml" />
<tool file="filters/compare.xml" />
<tool file="new_operations/subtract_query.xml" />
<tool file="stats/grouping.xml" />
</section>
<section id="features" name="Extract Features">
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
</section>
<section id="fetchSeq" name="Fetch Sequences">
<tool file="extract/extract_genomic_dna.xml" />
</section>
<section id="fetchAlign" name="Fetch Alignments">
<tool file="maf/interval2maf_pairwise.xml" />
<tool file="maf/interval2maf.xml" />
<tool file="maf/interval_maf_to_merged_fasta.xml" />
<tool file="maf/genebed_maf_to_fasta.xml" />
<tool file="maf/maf_stats.xml" />
<tool file="maf/maf_thread_for_species.xml" />
<tool file="maf/maf_limit_to_species.xml" />
<tool file="maf/maf_limit_size.xml" />
<tool file="maf/maf_by_block_number.xml" />
<tool file="maf/maf_filter.xml" />
<tool file="maf/maf_reverse_complement.xml" />
</section>
<section id="scores" name="Get Genomic Scores">
<tool file="stats/wiggle_to_simple.xml" />
<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
</section>
<section id="bxops" name="Operate on Genomic Intervals">
<tool file="new_operations/intersect.xml" />
<tool file="new_operations/subtract.xml" />
<tool file="new_operations/merge.xml" />
<tool file="new_operations/concat.xml" />
<tool file="new_operations/basecoverage.xml" />
<tool file="new_operations/coverage.xml" />
<tool file="new_operations/complement.xml" />
<tool file="new_operations/cluster.xml" id="cluster" />
<tool file="new_operations/join.xml" />
<tool file="new_operations/get_flanks.xml" />
<tool file="new_operations/flanking_features.xml" />
<tool file="annotation_profiler/annotation_profiler.xml" />
</section>
<section id="stats" name="Statistics">
<tool file="stats/gsummary.xml" />
<tool file="filters/uniq.xml" />
<tool file="stats/cor.xml" />
<tool file="stats/generate_matrix_for_pca_lda.xml" />
<tool file="stats/lda_analy.xml" />
<tool file="stats/plot_from_lda.xml" />
</section>
<section id="plots" name="Graph/Display Data">
<tool file="plotting/histogram2.xml" />
<tool file="plotting/scatterplot.xml" />
<tool file="plotting/boxplot.xml" />
<tool file="visualization/build_ucsc_custom_track.xml" />
<tool file="maf/vcf_to_maf_customtrack.xml" />
<tool file="mutation/visualize.xml" />
</section>
<section id="regVar" name="Regional Variation">
<tool file="regVariation/windowSplitter.xml" />
<tool file="regVariation/featureCounter.xml" />
<tool file="regVariation/WeightedAverage.xml" />
<tool file="regVariation/quality_filter.xml" />
<tool file="regVariation/maf_cpg_filter.xml" />
<tool file="regVariation/getIndels_2way.xml" />
<tool file="regVariation/getIndelRates_3way.xml" />
<tool file="regVariation/substitutions.xml" />
<tool file="regVariation/substitution_rates.xml" />
<tool file="regVariation/microsats_alignment_level.xml" />
<tool file="regVariation/microsats_mutability.xml" />
</section>
<section id="multReg" name="Multiple regression">
<tool file="regVariation/linear_regression.xml" />
<tool file="regVariation/logistic_regression_vif.xml" />
<tool file="regVariation/best_regression_subsets.xml" />
<tool file="regVariation/rcve.xml" />
<tool file="regVariation/partialR_square.xml" />
</section>
<section id="multVar" name="Multivariate Analysis">
<tool file="multivariate_stats/pca.xml" />
<tool file="multivariate_stats/cca.xml" />
<tool file="multivariate_stats/kpca.xml" />
<tool file="multivariate_stats/kcca.xml" />
</section>
<section id="clustal" name="Multiple Alignments">
<tool file="rgenetics/rgClustalw.xml" />
</section>
<section id="hgv" name="Phenotype Association">
<tool file="evolution/codingSnps.xml" />
<tool file="evolution/add_scores.xml" />
<tool file="phenotype_association/sift.xml" />
<tool file="phenotype_association/linkToGProfile.xml" />
<tool file="phenotype_association/linkToDavid.xml" />
<tool file="phenotype_association/snpFreq.xml" />
<tool file="phenotype_association/ldtools.xml" />
<tool file="phenotype_association/pass.xml" />
<tool file="phenotype_association/gpass.xml" />
<tool file="phenotype_association/beam.xml" />
<tool file="phenotype_association/lps.xml" />
<tool file="phenotype_association/master2pg.xml" />
<tool file="phenotype_association/vcf2pgSnp.xml" />
</section>
<label id="ngs" text="NGS Toolbox Beta" />
<section id="cshl_library_information" name="NGS: QC and manipulation">
<label id="illumina" text="Illumina data" />
<label id="454" text="Roche-454 data" />
<tool file="metag_tools/short_reads_figure_score.xml" />
<tool file="metag_tools/short_reads_trim_seq.xml" />
<label id="solid" text="AB-SOLiD data" />
<tool file="next_gen_conversion/solid2fastq.xml" />
<tool file="solid_tools/solid_qual_stats.xml" />
<tool file="solid_tools/solid_qual_boxplot.xml" />
<label id="generic_fastq" text="Generic FASTQ manipulation" />
<label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" />
</section>
<section id="ngs_mapping" name="NGS: Mapping">
<label id="illumina" text="Illumina" />
<label id="roche_454" text="Roche-454" />
<tool file="metag_tools/megablast_wrapper.xml" />
<tool file="metag_tools/megablast_xml_parser.xml" />
<label id="ab_solid" text="AB-SOLiD" />
</section>
<section id="samtools" name="NGS: SAM Tools">
</section>
<section id="gatk" name="NGS: GATK Tools (beta)">
<label id="gatk_bam_utilities" text="Alignment Utilities" />
<tool file="gatk/depth_of_coverage.xml" />
<tool file="gatk/print_reads.xml" />
<label id="gatk_realignment" text="Realignment" />
<tool file="gatk/realigner_target_creator.xml" />
<tool file="gatk/indel_realigner.xml" />
<label id="gatk_recalibration" text="Base Recalibration" />
<tool file="gatk/count_covariates.xml" />
<tool file="gatk/table_recalibration.xml" />
<tool file="gatk/analyze_covariates.xml" />
<label id="gatk_genotyping" text="Genotyping" />
<tool file="gatk/unified_genotyper.xml" />
<label id="gatk_annotation" text="Annotation" />
<tool file="gatk/variant_annotator.xml" />
<label id="gatk_filtration" text="Filtration" />
<tool file="gatk/variant_filtration.xml" />
<tool file="gatk/variant_select.xml" />
<label id="gatk_variant_quality_score_recalibration" text="Variant Quality Score Recalibration" />
<tool file="gatk/variant_recalibrator.xml" />
<tool file="gatk/variant_apply_recalibration.xml" />
<label id="gatk_variant_utilities" text="Variant Utilities" />
<tool file="gatk/variants_validate.xml" />
<tool file="gatk/variant_eval.xml" />
<tool file="gatk/variant_combine.xml" />
</section>
<section id="ngs-rna-tools" name="NGS: RNA Analysis">
<label id="rna_seq" text="RNA-seq" />
<label id="filtering" text="Filtering" />
</section>
</toolbox>