tool_conf.xml

<?xml version='1.0' encoding='utf-8'?>
<toolbox>
  <section name="Prok Pipeline" id="prok">
    <tool file="prokPipeline/simple_pipeline_config.xml" />
    <tool file="prokPipeline/prok_pipeline_setup.xml" />
    <tool file="prokPipeline/run_prok_pipeline.xml" />
    <tool file="prokPipeline/deliver_results.xml" />
    <tool file="prokPipeline/cleanup_area.xml" />
  </section>
  <section name="Viral Assembly and Annotation" id="viral_assembly_annotation">
    <tool file="viral_assembly_annotation/viral_assembly.xml" />
    <tool file="viral_assembly_annotation/VIGOR.xml" />
  </section>
  <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_test.xml" />
    <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
    <tool file="data_source/bx_browser.xml" />
    <tool file="data_source/microbial_import.xml" />
    <tool file="data_source/biomart.xml" />
    <tool file="data_source/biomart_test.xml" />
    <tool file="data_source/cbi_rice_mart.xml" />
    <tool file="data_source/gramene_mart.xml" />
    <tool file="data_source/fly_modencode.xml" />
    <tool file="data_source/flymine.xml" />
    <tool file="data_source/flymine_test.xml" />
    <tool file="data_source/modmine.xml" />
    <tool file="data_source/ratmine.xml" />
    <tool file="data_source/yeastmine.xml" />
    <tool file="data_source/metabolicmine.xml" />
    <tool file="data_source/worm_modencode.xml" />
    <tool file="data_source/wormbase.xml" />
    <tool file="data_source/wormbase_test.xml" />
    <tool file="data_source/eupathdb.xml" />
    <tool file="data_source/encode_db.xml" />
    <tool file="data_source/epigraph_import.xml" />
    <tool file="data_source/epigraph_import_test.xml" />
    <tool file="data_source/hbvar.xml" />
    <tool file="validation/fix_errors.xml" />
  </section>
  <section id="send" name="Send Data">
    <tool file="data_destination/epigraph.xml" />
    <tool file="data_destination/epigraph_test.xml" />
  </section>
  <section id="EncodeTools" name="ENCODE Tools">
    <tool file="encode/gencode_partition.xml" />
    <tool file="encode/random_intervals.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/cutWrapper.xml" />
    <tool file="filters/mergeCols.xml" />
    <tool file="filters/convert_characters.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="stats/dna_filtering.xml" />
    <tool file="new_operations/tables_arithmetic_operations.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="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="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/maf_split_by_species.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_reverse_complement.xml" />
    <tool file="maf/maf_filter.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" />
    <tool file="extract/phastOdds/phastOdds_tool.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="regVariation/compute_q_values.xml" />
    <label id="gff" text="GFF" />
		<tool file="stats/count_gff_features.xml" />
  </section>
  <!--
  Keep this section commented until all of the tools have functional tests
  <section name="Wavelet Analysis" id="dwt">
    <tool file="discreteWavelet/execute_dwt_IvC_all.xml" />
    <tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
    <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /> 
    <tool file="discreteWavelet/execute_dwt_var_perClass.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="regVar" name="Regional Variation">
    <tool file="regVariation/windowSplitter.xml" />
    <tool file="regVariation/featureCounter.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/best_regression_subsets.xml" />
    <tool file="regVariation/rcve.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="hyphy" name="Evolution">
    <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
    <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
    <tool file="hyphy/hyphy_dnds_wrapper.xml" />
    <tool file="evolution/codingSnps.xml" />
    <tool file="evolution/add_scores.xml" />
 </section>
  <section id="motifs" name="Motif Tools">
    <tool file="meme/meme.xml" />
  </section>
 <section id="tax_manipulation" name="Metagenomic analyses">
    <tool file="taxonomy/t2t_report.xml" />
    <tool file="taxonomy/t2ps_wrapper.xml" />
    <tool file="taxonomy/find_diag_hits.xml" />
    <tool file="taxonomy/lca.xml" />
    <tool file="taxonomy/poisson2test.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="ncbi_blast_plus_tools" name="NCBI BLAST+">
  </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_manipulation.xml" />
    <tool file="fastq/fastq_to_tabular.xml" />
    <tool file="fastq/tabular_to_fastq.xml" />
    </section>
  <section id="ngs_assembly" name="NGS: Assembly">
    <label id="velvet" text="Velvet" />
      <tool file="sr_assembly/velvetg.xml" />
      <tool file="sr_assembly/velveth.xml" />
  </section>
  <section id="solexa_tools" name="NGS: Mapping">
   <tool file="sr_mapping/bowtie2_wrapper.xml" />
   <tool file="metag_tools/megablast_wrapper.xml" />
   <tool file="metag_tools/megablast_xml_parser.xml" />
  </section>
  <section id="indel_analysis" name="NGS: Indel Analysis">
   <tool file="indels/sam_indel_filter.xml" />
   <tool file="indels/indel_sam2interval.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" />
      <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_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" />
  </section>
  <section id="peak_calling" name="NGS: Peak Calling">
   <tool file="peak_calling/macs_wrapper.xml" />
   <!-- <tool file="peak_calling/ccat_wrapper.xml" /> -->
   <tool file="genetrack/genetrack_indexer.xml" />
   <tool file="genetrack/genetrack_peak_prediction.xml" />
  </section>
  <!-- <section name="NGS: Simulation" id="ngs-simulation">
    <tool file="ngs_simulation/ngs_simulation.xml" />
  </section> -->
  <section id="rgdat" name="SNP/WGA: Data; Filters">
  <label id="rgimport" text="Data: Import and upload" />
    <tool file="data_source/upload.xml" />
    <tool file="data_source/access_libraries.xml" />
  </section>
  <section id="hgv" name="Human Genome Variation">
    <tool file="evolution/codingSnps.xml" />
    <tool file="evolution/add_scores.xml" />
  </section>
<!--
  This section can be uncommented on test, but the tools are not ready
  for main.
-->
<!--

  <section name="Genome Diversity" id="gd">
    <tool file="genome_diversity/extract_primers.xml" />
    <tool file="genome_diversity/select_snps.xml" />
    <tool file="genome_diversity/select_restriction_enzymes.xml" />
    <tool file="genome_diversity/extract_flanking_dna.xml" />
  </section>
-->
  <section id="vcf_tools" name="VCF Tools">
    <tool file="vcf_tools/intersect.xml" />
    <tool file="vcf_tools/annotate.xml" />
    <tool file="vcf_tools/filter.xml" />
    <tool file="vcf_tools/extract.xml" />
  </section>
</toolbox>