Changeset 1012:ccfcaf5e1352

Timestamp:

03/03/08 11:14:06 (10 months ago)

Author:

Greg Von Kuster <greg@bx.psu.edu>

branch:

default

convert_revision:

svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2370

Message:

Removed tool version directiories for some of the tools...the rest soon.

Files:

• tool_conf.xml.main (modified) (5 diffs)
• tool_conf.xml.sample (modified) (5 diffs)
• tools/encode/gencode_partition.xml (moved) (moved from tools/encode/gencode_partition1/1.0.0/gencode_partition.xml)
• tools/encode/random_intervals.xml (moved) (moved from tools/encode/random_intervals1/1.0.0/random_intervals.xml)
• tools/encode/random_intervals_no_bits.py (moved) (moved from tools/encode/random_intervals1/1.0.0/random_intervals_no_bits.py)
• tools/encode/split_by_partitions.py (moved) (moved from tools/encode/gencode_partition1/1.0.0/split_by_partitions.py)
• tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.pl (deleted)
• tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.xml (deleted)
• tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper_code.py (deleted)
• tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa (deleted)
• tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.py (deleted)
• tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.xml (deleted)
• tools/extract/extractAxt_wrapper.pl (moved) (moved from tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.pl)
• tools/extract/extractAxt_wrapper.xml (moved) (moved from tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.xml)
• tools/extract/extract_GFF_Features.py (moved) (moved from tools/extract/Extract_features1/1.0.0/extract_GFF_Features.py)
• tools/extract/extract_GFF_Features.xml (moved) (moved from tools/extract/Extract_features1/1.0.0/extract_GFF_Features.xml)
• tools/extract/extract_genomic_dna.py (moved) (moved from tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.py)
• tools/extract/extract_genomic_dna.xml (moved) (moved from tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.xml)
• tools/extract/extract_genomic_dna_code.py (moved) (moved from tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna_code.py)
• tools/extract/liftOver_wrapper.py (moved) (moved from tools/extract/liftOver1/1.0.0/liftOver_wrapper.py)
• tools/extract/liftOver_wrapper.xml (moved) (moved from tools/extract/liftOver1/1.0.0/liftOver_wrapper.xml)
• tools/extract/liftOver_wrapper_code.py (moved) (moved from tools/extract/liftOver1/1.0.0/liftOver_wrapper_code.py)
• tools/extract/phastOdds/get_scores_galaxy.py (added)
• tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/get_scores_galaxy.py (deleted)
• tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml (deleted)
• tools/extract/phastOdds/phastOdds_tool.xml (added)
• tools/fasta_tools/fasta_compute_length.py (moved) (moved from tools/fasta_tools/fasta_compute_length/1.0.0/fasta_compute_length.py)
• tools/fasta_tools/fasta_compute_length.xml (moved) (moved from tools/fasta_tools/fasta_compute_length/1.0.0/fasta_compute_length.xml)
• tools/fasta_tools/fasta_filter_by_length.py (moved) (moved from tools/fasta_tools/fasta_filter_by_length/1.0.0/fasta_filter_by_length.py)
• tools/fasta_tools/fasta_filter_by_length.xml (moved) (moved from tools/fasta_tools/fasta_filter_by_length/1.0.0/fasta_filter_by_length.xml)
• tools/fasta_tools/fasta_to_tabular.py (moved) (moved from tools/fasta_tools/fasta2tab/1.0.0/fasta_to_tabular.py)
• tools/fasta_tools/fasta_to_tabular.xml (moved) (moved from tools/fasta_tools/fasta2tab/1.0.0/fasta_to_tabular.xml)
• tools/fasta_tools/tabular_to_fasta.py (moved) (moved from tools/fasta_tools/tab2fasta/1.0.0/tabular_to_fasta.py)
• tools/fasta_tools/tabular_to_fasta.xml (moved) (moved from tools/fasta_tools/tab2fasta/1.0.0/tabular_to_fasta.xml)
• tools/filters/BedLike2Text.pl (moved) (moved from tools/filters/BedLike2Text1/1.0.0/BedLike2Text.pl)
• tools/filters/BedLike2Text.xml (moved) (moved from tools/filters/BedLike2Text1/1.0.0/BedLike2Text.xml)
• tools/filters/CreateInterval.pl (moved) (moved from tools/filters/createInterval/1.0.0/CreateInterval.pl)
• tools/filters/CreateInterval.xml (moved) (moved from tools/filters/createInterval/1.0.0/CreateInterval.xml)
• tools/filters/Interval2BedLike.pl (moved) (moved from tools/filters/Interval2Bed1/1.0.0/Interval2BedLike.pl)
• tools/filters/Interval2BedLike.xml (moved) (moved from tools/filters/Interval2Bed1/1.0.0/Interval2BedLike.xml)
• tools/filters/Text2BedLike.pl (moved) (moved from tools/filters/Text2BedLike1/1.0.0/Text2BedLike.pl)
• tools/filters/Text2BedLike.xml (moved) (moved from tools/filters/Text2BedLike1/1.0.0/Text2BedLike.xml)
• tools/filters/aggTrack.pl (moved) (moved from tools/filters/aggTrack1/1.0.0/aggTrack.pl)
• tools/filters/aggTrack.xml (moved) (moved from tools/filters/aggTrack1/1.0.0/aggTrack.xml)
• tools/filters/axt_to_concat_fasta.py (moved) (moved from tools/filters/axt_to_concat_fasta/1.0.0/axt_to_concat_fasta.py)
• tools/filters/axt_to_concat_fasta.xml (moved) (moved from tools/filters/axt_to_concat_fasta/1.0.0/axt_to_concat_fasta.xml)
• tools/filters/axt_to_fasta.py (moved) (moved from tools/filters/axt_to_fasta/1.0.0/axt_to_fasta.py)
• tools/filters/axt_to_fasta.xml (moved) (moved from tools/filters/axt_to_fasta/1.0.0/axt_to_fasta.xml)
• tools/filters/axt_to_lav.py (moved) (moved from tools/filters/axt_to_lav_1/1.0.0/axt_to_lav.py)
• tools/filters/axt_to_lav.xml (moved) (moved from tools/filters/axt_to_lav_1/1.0.0/axt_to_lav.xml)
• tools/filters/axt_to_lav_code.py (moved) (moved from tools/filters/axt_to_lav_1/1.0.0/axt_to_lav_code.py)
• tools/filters/bed2gff.xml (moved) (moved from tools/filters/bed2gff1/2.0.0/bed2gff.xml)
• tools/filters/bed2gff1/1.0.0/bed2gff.xml (deleted)
• tools/filters/bed2gff1/1.0.0/bed_to_gff_converter.py (deleted)
• tools/filters/bed_to_gff_converter.py (moved) (moved from tools/filters/bed2gff1/2.0.0/bed_to_gff_converter.py)
• tools/filters/catWrapper.xml (moved) (moved from tools/filters/cat1/1.0.0/catWrapper.xml)
• tools/filters/changeCase.pl (moved) (moved from tools/filters/ChangeCase1/1.0.0/changeCase.pl)
• tools/filters/changeCase.xml (moved) (moved from tools/filters/ChangeCase1/1.0.0/changeCase.xml)
• tools/filters/commWrapper.pl (moved) (moved from tools/filters/cat1/1.0.0/commWrapper.pl)
• tools/filters/commWrapper.xml (moved) (moved from tools/filters/Comm1/1.0.0/commWrapper.xml)
• tools/filters/compare.xml (moved) (moved from tools/filters/comp1/1.0.0/compare.xml)
• tools/filters/condense_characters.pl (moved) (moved from tools/filters/Condense_characters1/1.0.0/condense_characters.pl)
• tools/filters/condense_characters.xml (moved) (moved from tools/filters/Condense_characters1/1.0.0/condense_characters.xml)
• tools/filters/convert_characters.pl (moved) (moved from tools/filters/Convert_characters1/1.0.0/convert_characters.pl)
• tools/filters/convert_characters.xml (moved) (moved from tools/filters/Convert_characters1/1.0.0/convert_characters.xml)
• tools/filters/cutWrapper.pl (moved) (moved from tools/filters/Cut1/1.0.0/cutWrapper.pl)
• tools/filters/cutWrapper.xml (moved) (moved from tools/filters/Cut1/1.0.0/cutWrapper.xml)
• tools/filters/fileGrep.xml (moved) (moved from tools/filters/fileGrep1/1.0.0/fileGrep.xml)
• tools/filters/fixedValueColumn.pl (moved) (moved from tools/filters/addValue/1.0.0/fixedValueColumn.pl)
• tools/filters/fixedValueColumn.xml (moved) (moved from tools/filters/addValue/1.0.0/fixedValueColumn.xml)
• tools/filters/gff2bed.xml (moved) (moved from tools/filters/gff2bed1/1.0.0/gff2bed.xml)
• tools/filters/gff_to_bed_converter.py (moved) (moved from tools/filters/gff2bed1/1.0.0/gff_to_bed_converter.py)
• tools/filters/grep.py (moved) (moved from tools/filters/Grep1/1.0.0/grep.py)
• tools/filters/grep.xml (moved) (moved from tools/filters/Grep1/1.0.0/grep.xml)
• tools/filters/headWrapper.pl (moved) (moved from tools/filters/Show_beginning1/1.0.0/headWrapper.pl)
• tools/filters/headWrapper.xml (moved) (moved from tools/filters/Show_beginning1/1.0.0/headWrapper.xml)
• tools/filters/join.py (moved) (moved from tools/filters/join1/2.0.0/join.py)
• tools/filters/join1/1.0.0/joinWrapper.pl (deleted)
• tools/filters/join1/1.0.0/joiner.xml (deleted)
• tools/filters/joinWrapper.pl (moved) (moved from tools/filters/comp1/1.0.0/joinWrapper.pl)
• tools/filters/joiner.xml (moved) (moved from tools/filters/join1/2.0.0/joiner.xml)
• tools/filters/joiner2.xml (moved) (moved from tools/filters/joiner2/1.0.0/joiner2.xml)
• tools/filters/lav_to_bed.py (moved) (moved from tools/filters/lav_to_bed1/1.0.0/lav_to_bed.py)
• tools/filters/lav_to_bed.xml (moved) (moved from tools/filters/lav_to_bed1/1.0.0/lav_to_bed.xml)
• tools/filters/lav_to_bed_code.py (moved) (moved from tools/filters/lav_to_bed1/1.0.0/lav_to_bed_code.py)
• tools/filters/pasteWrapper.pl (moved) (moved from tools/filters/Paste1/1.0.0/pasteWrapper.pl)
• tools/filters/pasteWrapper.xml (moved) (moved from tools/filters/Paste1/1.0.0/pasteWrapper.xml)
• tools/filters/pasteWrapper_code.py (moved) (moved from tools/filters/Paste1/1.0.0/pasteWrapper_code.py)
• tools/filters/random_lines.py (moved) (moved from tools/filters/random_lines1/1.0.0/random_lines.py)
• tools/filters/random_lines.xml (moved) (moved from tools/filters/random_lines1/1.0.0/random_lines.xml)
• tools/filters/remove_beginning.pl (moved) (moved from tools/filters/Remove_beginning1/1.0.0/remove_beginning.pl)
• tools/filters/remove_beginning.xml (moved) (moved from tools/filters/Remove_beginning1/1.0.0/remove_beginning.xml)
• tools/filters/sorter.py (moved) (moved from tools/filters/sort1/1.0.0/sorter.py)
• tools/filters/sorter.xml (moved) (moved from tools/filters/sort1/1.0.0/sorter.xml)
• tools/filters/srg2wig.pl (moved) (moved from tools/filters/srg2wig1/1.0.0/srg2wig.pl)
• tools/filters/srg2wig.xml (moved) (moved from tools/filters/srg2wig1/1.0.0/srg2wig.xml)
• tools/filters/tailWrapper.pl (moved) (moved from tools/filters/Show_tail1/1.0.0/tailWrapper.pl)
• tools/filters/tailWrapper.xml (moved) (moved from tools/filters/Show_tail1/1.0.0/tailWrapper.xml)
• tools/filters/ucsc_gene_bed_to_exon_bed.py (moved) (moved from tools/filters/gene2exon1/1.0.0/ucsc_gene_bed_to_exon_bed.py)
• tools/filters/ucsc_gene_bed_to_exon_bed.xml (moved) (moved from tools/filters/gene2exon1/1.0.0/ucsc_gene_bed_to_exon_bed.xml)
• tools/filters/ucsc_gene_bed_to_intron_bed.py (moved) (moved from tools/filters/gene2intron1/1.0.0/ucsc_gene_bed_to_intron_bed.py)
• tools/filters/ucsc_gene_bed_to_intron_bed.xml (moved) (moved from tools/filters/gene2intron1/1.0.0/ucsc_gene_bed_to_intron_bed.xml)
• tools/filters/ucsc_gene_table_to_intervals.py (moved) (moved from tools/filters/ucsc_gene_table_to_intervals1/1.0.0/ucsc_gene_table_to_intervals.py)
• tools/filters/ucsc_gene_table_to_intervals.xml (moved) (moved from tools/filters/ucsc_gene_table_to_intervals1/1.0.0/ucsc_gene_table_to_intervals.xml)
• tools/filters/uniq.py (moved) (moved from tools/filters/Count1/1.0.0/uniq.py)
• tools/filters/uniq.xml (moved) (moved from tools/filters/Count1/1.0.0/uniq.xml)
• tools/hyphy/hyphy_branch_lengths_wrapper.py (moved) (moved from tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.py)
• tools/hyphy/hyphy_branch_lengths_wrapper.xml (moved) (moved from tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml)
• tools/hyphy/hyphy_dnds_wrapper.py (moved) (moved from tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.py)
• tools/hyphy/hyphy_dnds_wrapper.xml (moved) (moved from tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml)
• tools/hyphy/hyphy_nj_tree_wrapper.py (moved) (moved from tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.py)
• tools/hyphy/hyphy_nj_tree_wrapper.xml (moved) (moved from tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.xml)
• tools/maf/Interval2Maf_pairwise1/1.0.0/interval2maf.py (deleted)
• tools/maf/Interval_Maf_Merged_Fasta2/1.0.0/interval_maf_to_merged_fasta.py (deleted)
• tools/maf/genebed_maf_to_fasta.xml (moved) (moved from tools/maf/GeneBed_Maf_Fasta2/1.0.0/genebed_maf_to_fasta.xml)
• tools/maf/interval2maf.py (moved) (moved from tools/maf/Interval2Maf1/1.0.0/interval2maf.py)
• tools/maf/interval2maf.xml (moved) (moved from tools/maf/Interval2Maf1/1.0.0/interval2maf.xml)
• tools/maf/interval2maf_pairwise.xml (moved) (moved from tools/maf/Interval2Maf_pairwise1/1.0.0/interval2maf_pairwise.xml)
• tools/maf/interval_maf_to_merged_fasta.py (moved) (moved from tools/maf/GeneBed_Maf_Fasta2/1.0.0/interval_maf_to_merged_fasta.py)
• tools/maf/interval_maf_to_merged_fasta.xml (moved) (moved from tools/maf/Interval_Maf_Merged_Fasta2/1.0.0/interval_maf_to_merged_fasta.xml)
• tools/maf/maf_by_block_number.py (moved) (moved from tools/maf/maf_by_block_number1/1.0.0/maf_by_block_number.py)
• tools/maf/maf_by_block_number.xml (moved) (moved from tools/maf/maf_by_block_number1/1.0.0/maf_by_block_number.xml)
• tools/maf/maf_filter.py (moved) (moved from tools/maf/MAF_filter/1.0.0/maf_filter.py)
• tools/maf/maf_filter.xml (moved) (moved from tools/maf/MAF_filter/1.0.0/maf_filter.xml)
• tools/maf/maf_limit_size.py (moved) (moved from tools/maf/maf_limit_size1/1.0.0/maf_limit_size.py)
• tools/maf/maf_limit_size.xml (moved) (moved from tools/maf/maf_limit_size1/1.0.0/maf_limit_size.xml)
• tools/maf/maf_limit_to_species.py (moved) (moved from tools/maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.py)
• tools/maf/maf_limit_to_species.xml (moved) (moved from tools/maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.xml)
• tools/maf/maf_reverse_complement.py (moved) (moved from tools/maf/MAF_Reverse_Complement_1/1.0.0/maf_reverse_complement.py)
• tools/maf/maf_reverse_complement.xml (moved) (moved from tools/maf/MAF_Reverse_Complement_1/1.0.0/maf_reverse_complement.xml)
• tools/maf/maf_stats.py (moved) (moved from tools/maf/maf_stats1/1.0.0/maf_stats.py)
• tools/maf/maf_stats.xml (moved) (moved from tools/maf/maf_stats1/1.0.0/maf_stats.xml)
• tools/maf/maf_stats_code.py (moved) (moved from tools/maf/maf_stats1/1.0.0/maf_stats_code.py)
• tools/maf/maf_thread_for_species.py (moved) (moved from tools/maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.py)
• tools/maf/maf_thread_for_species.xml (moved) (moved from tools/maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.xml)
• tools/maf/maf_to_bed.py (moved) (moved from tools/maf/MAF_To_BED1/1.0.0/maf_to_bed.py)
• tools/maf/maf_to_bed.xml (moved) (moved from tools/maf/MAF_To_BED1/1.0.0/maf_to_bed.xml)
• tools/maf/maf_to_bed_code.py (moved) (moved from tools/maf/MAF_To_BED1/1.0.0/maf_to_bed_code.py)
• tools/maf/maf_to_fasta.xml (moved) (moved from tools/maf/MAF_To_Fasta1/1.0.0/maf_to_fasta.xml)
• tools/maf/maf_to_fasta_concat.py (moved) (moved from tools/maf/MAF_To_Fasta1/1.0.0/maf_to_fasta_concat.py)
• tools/maf/maf_to_fasta_multiple_sets.py (moved) (moved from tools/maf/MAF_To_Fasta1/1.0.0/maf_to_fasta_multiple_sets.py)
• tools/metag_tools/blat_wrapper.py (moved) (moved from tools/metag_tools/blat_wrapper/1.0.0/blat_wrapper.py)
• tools/metag_tools/blat_wrapper.xml (moved) (moved from tools/metag_tools/blat_wrapper/1.0.0/blat_wrapper.xml)
• tools/metag_tools/megablast_wrapper.py (moved) (moved from tools/metag_tools/megablast_wrapper/1.0.0/megablast_wrapper.py)
• tools/metag_tools/megablast_wrapper.xml (moved) (moved from tools/metag_tools/megablast_wrapper/1.0.0/megablast_wrapper.xml)
• tools/metag_tools/short_reads_figure_length.py (moved) (moved from tools/metag_tools/array_of_reads_length/1.0.0/short_reads_figure_length.py)
• tools/metag_tools/short_reads_figure_length.xml (moved) (moved from tools/metag_tools/array_of_reads_length/1.0.0/short_reads_figure_length.xml)
• tools/metag_tools/short_reads_figure_score.py (moved) (moved from tools/metag_tools/quality_score_distribution/1.0.0/short_reads_figure_score.py)
• tools/metag_tools/short_reads_figure_score.xml (moved) (moved from tools/metag_tools/quality_score_distribution/1.0.0/short_reads_figure_score.xml)
• tools/metag_tools/short_reads_trim_seq.py (moved) (moved from tools/metag_tools/trim_reads/1.0.0/short_reads_trim_seq.py)
• tools/metag_tools/short_reads_trim_seq.xml (moved) (moved from tools/metag_tools/trim_reads/1.0.0/short_reads_trim_seq.xml)

tool_conf.xml.main

@@ -18 +18 @@
-  </section>
-  <section name="ENCODE Tools" id="EncodeTools">
-1/1.0.0/gencode_partition
-1/1.0.0/random_intervals
+
+
-  </section>
-  <section name="Lift-Over" id="liftOver">
-1/1.0.0/liftOver
+
-  </section>
-  <section name="Text Manipulation" id="textutil">
-addValue/1.0.0/
+
-    <tool file="stats/Add_a_column1/1.0.0/column_maker.xml" />
-1/1.0.0/cat
-Condense_characters1/1.0.0/
-Convert_characters1/1.0.0/
-createInterval/1.0.0/
-Cut1/1.0.0/
-ChangeCase1/1.0.0/
-Paste1/1.0.0/
-Remove_beginning1/1.0.0/
-Show_beginning1/1.0.0/
-Show_tail1/1.0.0/
+
+
+
+
+
+
+
+
+
+
-  </section>
-  <section name="Filter and Sort" id="filter">
-    <tool file="stats/Filter1/1.0.0/filtering.xml" />
-1/1.0.0/sort
-Grep1/1.0.0/
+
+
-  </section>
-  <section name="Join, Subtract and Group" id="group">
-1/2.0.0/join
-1/1.0.0/comp
+
+
-    <tool file="new_operations/subtract_query1/1.0.0/subtract_query.xml"/>
-    <tool file="stats/Grouping1/1.0.0/grouping.xml" />   
-  </section>
-  <section name="Convert Formats" id="convert">
-1/2.0.0/bed2gff
-2tab/1.0.0/fasta
-1/1.0.0/gff2bed
-MAF_To_BED1/1.0.0/
-MAF_To_Fasta1/1.0.0/
-2fasta/1.0.0/tab
+
+
+
+
+
+
-  </section>
-  <section name="Extract Features" id="features">
-gene2exon1/1.0.0/
-Extract_features1/1.0.0/
+
+
-  </section>
-  <!--  
@@ -67 +67 @@
-  -->
-  <section name="Fetch Sequences" id="fetchSeq">
-Extract_genomic_DNA_1/2.0.0/
+
-  </section>
-  <section name="Fetch Alignments" id="fetchAlign">
-Interval2Maf_pairwise1/1.0.0/
-Interval2Maf1/1.0.0/
-Interval_Maf_Merged_Fasta2/1.0.0/
-GeneBed_Maf_Fasta2/1.0.0/
-1/1.0.0/maf_stats
-MAF_Thread_For_Species1/1.0.0/
-MAF_Limit_To_Species1/1.0.0/
-1/1.0.0/maf_limit_size
-1/1.0.0/maf_by_block_number
+
+
+
+
+
+
+
+
+
-    <!--    
-MAF_Reverse_Complement_1/1.0.0/
-MAF_filter/1.0.0/
+
+
-    -->
-  </section>
@@ -87 +87 @@
-    <tool file="stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml" />
-    <tool file="stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml" />
-for_intervals/1.0.0/phastOdds_
+
-  </section>
-  <section name="Operate on Genomic Intervals" id="bxops">
@@ -103 +103 @@
-  <section name="Statistics" id="stats">
-    <tool file="stats/Summary_Statistics1/1.0.0/gsummary.xml" />
-Count1/1.0.0/
+
-    <tool file="stats/cor2/1.0.0/cor.xml" /> 
-  </section>
@@ -124 +124 @@
-  </section>
- <section name="Evolution: HyPhy" id="hyphy">
-1/1.0.0/hyphy_branch_lengths_wrapper
-1/1.0.0/hyphy_nj_tree_wrapper
-1/1.0.0/hyphy_dnds_wrapper
+
+
+
- </section>
-  <section name="EMBOSS" id="EMBOSSLite">

tool_conf.xml.sample

@@ -22 +22 @@
-  </section>
-  <section name="ENCODE Tools" id="EncodeTools">
-1/1.0.0/gencode_partition
-1/1.0.0/random_intervals
+
+
-  </section>
-  <section name="Lift-Over" id="liftOver">
-1/1.0.0/liftOver
+
-  </section>
-  <section name="Text Manipulation" id="textutil">
-addValue/1.0.0/
+
-    <tool file="stats/Add_a_column1/1.0.0/column_maker.xml" />
-1/1.0.0/cat
-Condense_characters1/1.0.0/
-Convert_characters1/1.0.0/
-createInterval/1.0.0/
-Cut1/1.0.0/
-ChangeCase1/1.0.0/
-Paste1/1.0.0/
-Remove_beginning1/1.0.0/
-Show_beginning1/1.0.0/
-Show_tail1/1.0.0/
+
+
+
+
+
+
+
+
+
+
-  </section>
-  <section name="Filter and Sort" id="filter">
-    <tool file="stats/Filter1/1.0.0/filtering.xml" />
-1/1.0.0/sort
-Grep1/1.0.0/
+
+
-  </section>
-  <section name="Join, Subtract and Group" id="group">
-1/2.0.0/join
-1/1.0.0/comp
+
+
-    <tool file="new_operations/subtract_query1/1.0.0/subtract_query.xml"/>
-    <tool file="stats/Grouping1/1.0.0/grouping.xml" />   
-  </section>
-  <section name="Convert Formats" id="convert">
-/1.0.0/axt_to_concat_fasta
-/1.0.0/axt_to_fasta
-_1/1.0.0/axt_to_lav
-1/2.0.0/bed2gff
-2tab/1.0.0/fasta
-1/1.0.0/gff2bed
-1/1.0.0/lav_to_bed
-MAF_To_BED1/1.0.0/
-MAF_To_Fasta1/1.0.0/
-2fasta/1.0.0/tab
+
+
+
+
+
+
+
+
+
+
-  </section>
-  <section name="Extract Features" id="features">
-gene2exon1/1.0.0/
-Extract_features1/1.0.0/
+
+
-  </section>
-  <section name="Pattern-Matching" id="patmat">
@@ -73 +73 @@
-  </section>
-  <section name="Fetch Sequences" id="fetchSeq">
-Extract_genomic_DNA_1/2.0.0/
+
-  </section>
-  <section name="Fetch Alignments" id="fetchAlign">
-Interval2Maf_pairwise1/1.0.0/
-Interval2Maf1/1.0.0/
-Interval_Maf_Merged_Fasta2/1.0.0/
-GeneBed_Maf_Fasta2/1.0.0/
-1/1.0.0/maf_stats
-MAF_Thread_For_Species1/1.0.0/
-MAF_Limit_To_Species1/1.0.0/
-1/1.0.0/maf_limit_size
-1/1.0.0/maf_by_block_number
-MAF_Reverse_Complement_1/1.0.0/
-MAF_filter/1.0.0/
+
+
+
+
+
+
+
+
+
+
+
-  </section>
-  <section name="Get Genomic Scores" id="scores">
-    <tool file="stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml" />
-    <tool file="stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml" />
-for_intervals/1.0.0/phastOdds_
+
-  </section>
-  <section name="Operate on Genomic Intervals" id="bxops">
@@ -107 +107 @@
-  <section name="Statistics" id="stats">
-    <tool file="stats/Summary_Statistics1/1.0.0/gsummary.xml" />
-Count1/1.0.0/
+
-    <tool file="stats/cor2/1.0.0/cor.xml" /> 
-  </section>
@@ -127 +127 @@
-  </section>
- <section name="Evolution: HyPhy" id="hyphy">
-1/1.0.0/hyphy_branch_lengths_wrapper
-1/1.0.0/hyphy_nj_tree_wrapper
-1/1.0.0/hyphy_dnds_wrapper
+
+
+
- </section>
-  <!--
@@ -249 +249 @@
-  -->
-  <section name="FASTA manipulation" id="fasta_manipulation">
-/1.0.0/fasta_compute_length
-/1.0.0/fasta_filter_by_length
+
+
-  </section>
-  <section name="Short Read Analysis" id="short_read_analysis">
-trim_reads/1.0.0/
-/1.0.0/blat_wrapper
-/1.0.0/megablast_wrapper
+
+
+
-  </section>
-</toolbox>