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jianma committed c171edf

tool_conf.xml.cistrome

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tool_conf.xml.cistrome

     <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/ebi_sra.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/epigraph_import.xml" />
     <tool file="data_source/epigraph_import_test.xml" />
     <tool file="data_source/hbvar.xml" />
+    <tool file="genomespace/genomespace_file_browser_prod.xml" />
+    <tool file="genomespace/genomespace_importer.xml" />
     <tool file="validation/fix_errors.xml" />
-    <tool file="data_destination/epigraph_test.xml" />    
   </section>
+  <!--<section name="Send Data" id="send">
+    <tool file="data_destination/epigraph.xml" />
+    <tool file="data_destination/epigraph_test.xml" />
+    <tool file="genomespace/genomespace_exporter.xml" />
+  </section>
+  <section name="ENCODE Tools" id="EncodeTools">
+    <tool file="encode/gencode_partition.xml" />
+    <tool file="encode/random_intervals.xml" />
+  </section>
+  <section name="Lift-Over" id="liftOver">
+    <tool file="extract/liftOver_wrapper.xml" />
+  </section>-->
   <section name="Text Manipulation" id="textutil">
     <tool file="filters/fixedValueColumn.xml" />
     <tool file="stats/column_maker.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>
     <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="new_operations/column_join.xml" />
   </section>
   <section name="Convert Formats" id="convert">
-    <!--interval to bed converter enabled in Cistrome-->
-    <tool file="../lib/galaxy/datatypes/converters/interval_to_bed_converter.xml" />
     <tool file="filters/axt_to_concat_fasta.xml" />
     <tool file="filters/axt_to_fasta.xml" />
     <tool file="filters/axt_to_lav.xml" />
   <section name="Fetch Sequences" id="fetchSeq">
     <tool file="extract/extract_genomic_dna.xml" />
   </section>
+  <!--<section name="Fetch Alignments" id="fetchAlign">
+    <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 name="Get Genomic Scores" id="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 name="Operate on Genomic Intervals" id="bxops">
     <tool file="new_operations/intersect.xml" />
     <tool file="new_operations/subtract.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="Wavelet Analysis" id="dwt">
+    <tool file="discreteWavelet/execute_dwt_var_perFeature.xml" />
+    <!--
+    Keep this section/tools commented until all of the tools have functional tests
     <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_cor_aVb_all.xml" />
     <tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
+    -->
   </section>
   <section name="Graph/Display Data" id="plots">
     <tool file="plotting/histogram2.xml" />
   <section name="Regional Variation" id="regVar">
     <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/compute_motif_frequencies_for_all_motifs.xml" />
     <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
     <tool file="regVariation/draw_stacked_barplots.xml" />
-    <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />    
-    <tool file="regVariation/microsatellite_birthdeath.xml" />        
+    <!-- <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
+    <tool file="regVariation/microsatellite_birthdeath.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" />