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tool_conf-tut.xml
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<?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="genomespace/genomespace_file_browser_prod.xml" />
<tool file="genomespace/genomespace_importer.xml" />
<tool file="genomespace/genomespace_exporter.xml" />
</section>
<section id="EncodeTools" name="ENCODE Tools">
<tool file="encode/gencode_partition.xml" />
<tool file="encode/random_intervals.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="filter" name="Filter and Sort">
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.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" />
<tool file="new_operations/column_join.xml" />
</section>
<section id="convert" name="Convert Formats">
<tool file="filters/axt_to_concat_fasta.xml" />
<tool file="filters/axt_to_fasta.xml" />
<tool file="filters/axt_to_lav.xml" />
<tool file="filters/bed2gff.xml" />
<tool file="fasta_tools/fasta_to_tabular.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="filters/lav_to_bed.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="fastq/fastq_to_fasta.xml" />
<tool file="filters/wiggle_to_simple.xml" />
<tool file="filters/sff_extractor.xml" />
<tool file="filters/gtf2bedgraph.xml" />
<tool file="filters/wig_to_bigwig.xml" />
<tool file="filters/bed_to_bigbed.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" />
<tool file="stats/MINE.xml" />
<label id="gff" text="GFF" />
<tool file="stats/count_gff_features.xml" />
</section>
<section id="plots" name="Graph/Display Data">
<tool file="plotting/histogram2.xml" />
<tool file="plotting/scatterplot.xml" />
<tool file="plotting/bar_chart.xml" />
<tool file="plotting/boxplot.xml" />
<tool file="visualization/GMAJ.xml" />
<tool file="visualization/LAJ.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="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="NGS_QC" name="NGS: QC and manipulation">
<label id="fastqcsambam" text="FastQC: fastq/sam/bam" />
<tool file="rgenetics/rgFastQC.xml" />
<label id="illumina" text="Illumina fastq" />
<tool file="fastq/fastq_groomer.xml" />
<tool file="fastq/fastq_paired_end_splitter.xml" />
<tool file="fastq/fastq_paired_end_joiner.xml" />
<tool file="fastq/fastq_stats.xml" />
<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" />
<tool file="fastq/fastq_combiner.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" />
<tool file="fastq/fastq_filter.xml" />
<tool file="fastq/fastq_trimmer.xml" />
<tool file="fastq/fastq_trimmer_by_quality.xml" />
<tool file="fastq/fastq_masker_by_quality.xml" />
<tool file="fastq/fastq_paired_end_interlacer.xml" />
<tool file="fastq/fastq_paired_end_deinterlacer.xml" />
<tool file="fastq/fastq_manipulation.xml" />
<tool file="fastq/fastq_to_fasta.xml" />
<tool file="fastq/fastq_to_tabular.xml" />
<tool file="fastq/tabular_to_fastq.xml" />
<label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" />
</section>
<section id="indel_analysis" name="NGS: Indel Analysis">
<tool file="indels/sam_indel_filter.xml" />
<tool file="indels/indel_table.xml" />
<tool file="indels/indel_analysis.xml" />
</section>
<section id="ngs-rna-tools" name="NGS: RNA Analysis">
<label id="rna_seq" text="RNA-seq" />
<tool file="ngs_rna/tophat_wrapper.xml" />
<tool file="ngs_rna/tophat2_wrapper.xml" />
<tool file="ngs_rna/tophat_color_wrapper.xml" />
<tool file="ngs_rna/express_wrapper.xml" />
<!-- Trinity is very memory-intensive and should only be enabled/run
on instances with sufficient resources.
<label text="De novo Assembly" id="de_novo_assembly "/>
<tool file="ngs_rna/trinity_all.xml" />
-->
<label id="filtering" text="Filtering" />
<tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
</section>
<section id="samtools" name="NGS: SAM Tools">
</section>
<section id="gatk" name="NGS: GATK Tools">
<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>
</toolbox>