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<?xml version="1.0"?>
<toolbox>
  <section name="Get Data" id="getext">
    <tool file="data_source/upload.xml"/>
  </section>
  <section name="Text Manipulation" id="textutil">
    <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="filters/secure_hash_message_digest.xml" />
    <tool file="stats/dna_filtering.xml" />
    <tool file="new_operations/tables_arithmetic_operations.xml" />
  </section>
  <section name="Filter and Sort" id="filter">
    <tool file="stats/filtering.xml" />
    <tool file="filters/sorter.xml" />
    <tool file="filters/grep.xml" />
    
    <label text="GFF" id="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 name="Join, Subtract and Group" id="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 name="Convert Formats" id="convert">
    <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 name="Statistics" id="stats">
    <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/t_test_two_samples.xml" />
    <tool file="regVariation/compute_q_values.xml" />
    <tool file="stats/MINE.xml" />
    
    <label text="GFF" id="gff" />
    <tool file="stats/count_gff_features.xml" />
  </section>
  <section name="Graph/Display Data" id="plots">
    <tool file="plotting/histogram2.xml" />
    <tool file="plotting/scatterplot.xml" />
    <tool file="plotting/bar_chart.xml" />
    <tool file="plotting/xy_plot.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 name="Multiple regression" id="multReg">
    <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 name="Multivariate Analysis" id="multVar">
    <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>
  
<!-- 
        This is the MPDS 1.0.1 modules
    -->
  <label text="MPDS 1.0.1" id="mpds" />
  <section name="Module1_2_4 (Search Target Compound Fragment Library)" id="mpdssearch">
    <tool file="module_mpds_databases/mpdssearch.xml"/>
  </section>
  <section name="Module1 (Target Library)" id="tlib">
  </section>
  <section name="Module2 (Compound Library)" id="clib">
  </section>
  <section name="Module3 (File-Format Convertor)" id="ffc">
    <tool file="CADDSuite/galaxyconfigs/tools/Converter.xml" />
  </section>
  <section name="Module4 (Fragment Library)" id="flib">
  </section>
  <section name="Module5 (Descriptor Calculation)" id="disp">
    <!--  tool file="cdk/cdk.xml"/ -->
    <tool file="admetpred/cdk.xml"/>
  </section>
  <section name="Deepak (Descriptor Calculation)" id="dis">
    <tool file="cdk/cdk.xml"/>
    <tool file="PaDEL/padel.xml"/>
  </section>

  <section name="Module6 (QSAR)" id="qsar">
    <tool file="mcqsar/mcqsar.xml"/>
    <tool file="mcqsar/mcqsar_prediction.xml"/>
  </section>
 <section name="Module7 (Docking)" id="docking_prgram">
<tool file="Docking/receptor_pdbqt.xml"/>
</section>
  <section name="Module8 (Filters)" id="filt">
    <tool file="admetpredictor/descal.xml"/>
    <tool file="admetpredictor/DruLiTo.xml"/>
    <tool file="admetpredictor/Split1.xml"/>
    <tool file="admetpredictor/BCSclass.xml" />
  </section>
  <section name="Module9 (Visualization)" id="visu">
    <tool file="module9/view3d.xml"/>
  </section>   
<!--
<section name="Module1 Docking (using Autodock)" id="autodock">
<tool file="autodock/receptor_pdbqt.xml"/>
</section>
<section name="Module2: Descriptor Processing" id="module2">
<tool file="module2/upload.xml"/>
<tool file="filters/convert_characters.xml" />
<tool file="module2/2d_to_3d.xml"/>
<tool file="module2/desc_calc.xml"/>
<tool file="module2/filtering.xml"/>
<tool file="module2/inputqsar.xml"/>
<tool file="module2/view3d.xml"/>
</section>
<section name="module3 Database Library" id="module3">
</section>
	<section name="Module4 Build Predictive Model" id="pmodel">
        <tool file="pmodel/tool1.xml" />
        <tool file="pmodel/tool2.xml" />
        <tool file="pmodel/tool3.xml" />
</section>
<section name="Module5 admetpred" id="admetpred">
        <tool file="admetpred/upload.xml"/>
        <tool file="admetpred/descal.xml"/>
        <tool file="admetpred/dlf.xml"/>
        <tool file="admetpred/split1.xml"/>
        <tool file="admetpred/cdk.xml"/>
        <tool file="admetpred/metapred.xml"/>
</section>
<section name="Module6 Docking Results Analysis Tools" id="drat">
        <tool file="drat/filter1.xml" />
        <tool file="drat/filter2.xml" />
        <tool file="drat/plotligplot.xml" />
</section>
 -->

</toolbox>