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galaxy/tool_conf.xml.sample
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Guruprasad Anada 4919d2d048 Adding new tool "Extract features from GFF file" under Fetch Sequences and Alignments section. 
Have not been able to get this tool to pass functional test as test support with the new conditional constructs is yet to be worked out.
2007-06-19 14:04:41 +00:00

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<?xml version="1.0"?>
<toolbox>
<section name="Get Data" id="getext">
<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_proxy.xml"/>
<tool file="data_source/ucsc_testproxy.xml" /> -->
<tool file="data_source/ucsc_archaea.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/encode_db.xml" />
<tool file="data_source/hbvar.xml" />
<tool file="validation/fix_errors.xml" />
</section>
<section name="Get ENCODE Data" id="encode">
<tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/>
<tool file="data_source/encode_import_genes_and_transcripts.xml"/>
<tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/>
<tool file="data_source/encode_import_transcription_regulation.xml"/>
<tool file="data_source/encode_import_all_latest_datasets.xml" />
<tool file="data_source/encode_import_gencode.xml" />
</section>
<section name="ENCODE Tools" id="EncodeTools">
<tool file="extract/interval2maf.xml" />
<tool file="extract/phastOdds/phastOdds_tool.xml" />
<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
<tool file="encode/gencode_partition.xml" />
<tool file="encode/random_intervals.xml" />
</section>
<section name="Edit Queries" id="textutil">
<tool file="filters/fixedValueColumn.xml" />
<!-- <tool file="operations/combineLists.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/CreateInterval.xml" />
<tool file="filters/cutWrapper.xml" />
<tool file="filters/pasteWrapper.xml" />
<tool file="filters/remove_beginning.xml" />
<tool file="filters/headWrapper.xml" />
<tool file="filters/tailWrapper.xml" />
</section>
<section name="Filter, Sort, Join, Compare, Subtract" id="filter">
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.xml" />
<tool file="filters/joiner.xml" />
<tool file="filters/compare.xml"/>
<tool file="new_operations/subtract_query.xml"/>
</section>
<section name="Convert Formats" id="convert">
<tool file="filters/maf/maf_to_fasta_multiple_sets.xml" />
<tool file="filters/maf/maf_to_fasta_concat.xml" />
<tool file="filters/maf/maf_to_bed.xml" />
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="filters/bed2gff.xml" />
<tool file="filters/axt_to_fasta.xml" />
<tool file="filters/axt_to_concat_fasta.xml" />
<tool file="filters/axt_to_lav.xml" />
<tool file="filters/lav_to_bed.xml" />
</section>
<section name="Pattern-Matching" id="patmat">
<tool file="patmat/findcluster_mysql.xml" />
</section>
<section name="Fetch Sequences and Alignments" id="extract">
<tool file="extract/fasta-subseq-wrapper.xml" />
<tool file="extract/twoBitToFa_wrapper.xml" />
<tool file="extract/extractAxt_wrapper.xml" />
<tool file="extract/interval2maf_pairwise.xml" />
<tool file="extract/interval2maf.xml" />
<tool file="extract/user_interval2maf.xml" />
<tool file="extract/interval_maf_to_merged_fasta.xml" />
<tool file="extract/interval_maf_to_merged_fasta_user.xml" />
<tool file="extract/genebed_maf_to_fasta.xml"/>
<tool file="extract/genebed_maf_to_fasta_user.xml"/>
<tool file="filters/maf/maf_stats.xml"/>
<tool file="filters/maf/maf_limit_to_species.xml"/>
<tool file="filters/maf/maf_limit_size.xml"/>
<tool file="filters/maf/maf_by_block_number.xml"/>
<tool file="extract/extract_GFF_Features.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" id="intersect" />
<tool file="new_operations/subtract.xml" id="subtract" />
<tool file="new_operations/merge.xml" id="merge" />
<tool file="new_operations/concat.xml" id="concat" />
<tool file="new_operations/basecoverage.xml" id="basecoverage" />
<tool file="new_operations/coverage.xml" id="coverage" />
<tool file="new_operations/complement.xml" id="complement" />
<tool file="new_operations/cluster.xml" id="cluster" />
<tool file="new_operations/join.xml" id="join" />
<tool file="new_operations/get_flanks.xml" />
</section>
<section name="Statistics" id="stats">
<tool file="stats/gsummary.xml" />
<tool file="filters/uniq.xml" />
<tool file="stats/cor.xml" />
</section>
<section name="Graph/Display Data" id="plots">
<tool file="plotting/histogram2.xml" />
<tool file="plotting/scatterplot.xml" />
<tool file="plotting/xy_plot.xml" />
<tool file="visualization/GMAJ.xml" />
<tool file="visualization/LAJ.xml" />
<tool file="data_source/show_in_ucsc.xml" />
<tool file="visualization/build_ucsc_custom_track.xml" />
</section>
<section name="EMBOSS" id="EMBOSSLite">
<tool file="emboss/emboss_cai.xml" />
<tool file="emboss/emboss_cai_custom.xml" />
<!-- <tool file="emboss/emboss_codcmp.xml" /> -->
<tool file="emboss/emboss_compseq.xml" />
<!-- <tool file="emboss/emboss_cpgplot.xml" /> -->
<tool file="emboss/emboss_cpgreport.xml" />
<tool file="emboss/emboss_cusp.xml" />
<tool file="emboss/emboss_cutseq.xml" />
<!-- <tool file="emboss/emboss_dan.xml" /> -->
<tool file="emboss/emboss_einverted.xml" />
<tool file="emboss/emboss_equicktandem.xml" />
<tool file="emboss/emboss_est2genome.xml" />
<tool file="emboss/emboss_etandem.xml" />
<!-- <tool file="emboss/emboss_freak.xml" /> -->
<tool file="emboss/emboss_fuzznuc.xml" />
<tool file="emboss/emboss_fuzztran.xml" />
<tool file="emboss/emboss_getorf.xml" />
<tool file="emboss/emboss_isochore.xml" />
<tool file="emboss/emboss_msbar.xml" />
<tool file="emboss/emboss_needle.xml" />
<!-- <tool file="emboss/emboss_newcpgreport.xml" /> -->
<tool file="emboss/emboss_newcpgseek.xml" />
<tool file="emboss/emboss_newseq.xml" />
<tool file="emboss/emboss_notseq.xml" />
<tool file="emboss/emboss_nthseq.xml" />
<tool file="emboss/emboss_palindrome.xml" />
<tool file="emboss/emboss_pasteseq.xml" />
<tool file="emboss/emboss_plotorf.xml" />
<tool file="emboss/emboss_polydot.xml" />
<tool file="emboss/emboss_prettyseq.xml" />
<tool file="emboss/emboss_primersearch.xml" />
<tool file="emboss/emboss_revseq.xml" />
<tool file="emboss/emboss_seqmatchall.xml" />
<!-- <tool file="emboss/emboss_showorf.xml" /> -->
<tool file="emboss/emboss_shuffleseq.xml" />
<tool file="emboss/emboss_sirna.xml" />
<tool file="emboss/emboss_sixpack.xml" />
<tool file="emboss/emboss_splitter.xml" />
<!-- <tool file="emboss/emboss_stretcher.xml" /> -->
<tool file="emboss/emboss_supermatcher.xml" />
<tool file="emboss/emboss_syco.xml" />
<tool file="emboss/emboss_tranalign.xml" />
<tool file="emboss/emboss_transeq.xml" />
<tool file="emboss/emboss_trimest.xml" />
<tool file="emboss/emboss_trimseq.xml" />
<tool file="emboss/emboss_union.xml" />
<tool file="emboss/emboss_vectorstrip.xml" />
<tool file="emboss/emboss_water.xml" />
<tool file="emboss/emboss_wobble.xml" />
<tool file="emboss/emboss_wordcount.xml" />
<tool file="emboss/emboss_wordmatch.xml" />
<tool file="emboss/emboss_backtranseq.xml" />
<tool file="emboss/emboss_biosed.xml" />
<tool file="emboss/emboss_charge.xml" />
<tool file="emboss/emboss_checktrans.xml" />
</section>
<!--
<section name="Run EMBOSS nucleotide" id="EMBOSSnucleotide">
<tool file="emboss/emboss_biosed.xml" />
<tool file="emboss/emboss_btwisted.xml" />
<tool file="emboss/emboss_cai.xml" />
<tool file="emboss/emboss_chaos.xml" />
<tool file="emboss/emboss_chips.xml" />
<tool file="emboss/emboss_codcmp.xml" />
<tool file="emboss/emboss_coderet.xml" />
<tool file="emboss/emboss_compseq.xml" />
<tool file="emboss/emboss_cpgplot.xml" />
<tool file="emboss/emboss_cpgreport.xml" />
<tool file="emboss/emboss_cusp.xml" />
<tool file="emboss/emboss_cutseq.xml" />
<tool file="emboss/emboss_dan.xml" />
<tool file="emboss/emboss_degapseq.xml" />
<tool file="emboss/emboss_descseq.xml" />
<tool file="emboss/emboss_diffseq.xml" />
<tool file="emboss/emboss_dotmatcher.xml" />
<tool file="emboss/emboss_dotpath.xml" />
<tool file="emboss/emboss_dottup.xml" />
<tool file="emboss/emboss_einverted.xml" />
<tool file="emboss/emboss_equicktandem.xml" />
<tool file="emboss/emboss_est2genome.xml" />
<tool file="emboss/emboss_etandem.xml" />
<tool file="emboss/emboss_extractfeat.xml" />
<tool file="emboss/emboss_extractseq.xml" />
<tool file="emboss/emboss_freak.xml" />
<tool file="emboss/emboss_fuzznuc.xml" />
<tool file="emboss/emboss_fuzztran.xml" />
<tool file="emboss/emboss_geecee.xml" />
<tool file="emboss/emboss_getorf.xml" />
<tool file="emboss/emboss_helixturnhelix.xml" />
<tool file="emboss/emboss_infoseq.xml" />
<tool file="emboss/emboss_isochore.xml" />
<tool file="emboss/emboss_marscan.xml" />
<tool file="emboss/emboss_maskfeat.xml" />
<tool file="emboss/emboss_maskseq.xml" />
<tool file="emboss/emboss_matcher.xml" />
<tool file="emboss/emboss_megamerger.xml" />
<tool file="emboss/emboss_merger.xml" />
<tool file="emboss/emboss_msbar.xml" />
<tool file="emboss/emboss_needle.xml" />
<tool file="emboss/emboss_newcpgreport.xml" />
<tool file="emboss/emboss_newcpgseek.xml" />
<tool file="emboss/emboss_newseq.xml" />
<tool file="emboss/emboss_noreturn.xml" />
<tool file="emboss/emboss_notseq.xml" />
<tool file="emboss/emboss_nthseq.xml" />
<tool file="emboss/emboss_palindrome.xml" />
<tool file="emboss/emboss_pasteseq.xml" />
<tool file="emboss/emboss_plotorf.xml" />
<tool file="emboss/emboss_polydot.xml" />
<tool file="emboss/emboss_prettyseq.xml" />
<tool file="emboss/emboss_primersearch.xml" />
<tool file="emboss/emboss_revseq.xml" />
<tool file="emboss/emboss_seqmatchall.xml" />
<tool file="emboss/emboss_seqret.xml" />
<tool file="emboss/emboss_showfeat.xml" />
<tool file="emboss/emboss_showorf.xml" />
<tool file="emboss/emboss_shuffleseq.xml" />
<tool file="emboss/emboss_sirna.xml" />
<tool file="emboss/emboss_sixpack.xml" />
<tool file="emboss/emboss_skipseq.xml" />
<tool file="emboss/emboss_splitter.xml" />
<tool file="emboss/emboss_stretcher.xml" />
<tool file="emboss/emboss_stssearch.xml" />
<tool file="emboss/emboss_supermatcher.xml" />
<tool file="emboss/emboss_syco.xml" />
<tool file="emboss/emboss_tcode.xml" />
<tool file="emboss/emboss_textsearch.xml" />
<tool file="emboss/emboss_tranalign.xml" />
<tool file="emboss/emboss_transeq.xml" />
<tool file="emboss/emboss_trimest.xml" />
<tool file="emboss/emboss_trimseq.xml" />
<tool file="emboss/emboss_twofeat.xml" />
<tool file="emboss/emboss_union.xml" />
<tool file="emboss/emboss_vectorstrip.xml" />
<tool file="emboss/emboss_water.xml" />
<tool file="emboss/emboss_wobble.xml" />
<tool file="emboss/emboss_wordcount.xml" />
<tool file="emboss/emboss_wordmatch.xml" />
</section>
<section name="Run EMBOSS protein" id="EMBOSSprotein">
<tool file="emboss/emboss_antigenic.xml" />
<tool file="emboss/emboss_backtranseq.xml" />
<tool file="emboss/emboss_biosed.xml" />
<tool file="emboss/emboss_chaos.xml" />
<tool file="emboss/emboss_charge.xml" />
<tool file="emboss/emboss_checktrans.xml" />
<tool file="emboss/emboss_coderet.xml" />
<tool file="emboss/emboss_compseq.xml" />
<tool file="emboss/emboss_cutseq.xml" />
<tool file="emboss/emboss_degapseq.xml" />
<tool file="emboss/emboss_descseq.xml" />
<tool file="emboss/emboss_diffseq.xml" />
<tool file="emboss/emboss_digest.xml" />
<tool file="emboss/emboss_dotmatcher.xml" />
<tool file="emboss/emboss_dotpath.xml" />
<tool file="emboss/emboss_dottup.xml" />
<tool file="emboss/emboss_epestfind.xml" />
<tool file="emboss/emboss_extractfeat.xml" />
<tool file="emboss/emboss_extractseq.xml" />
<tool file="emboss/emboss_freak.xml" />
<tool file="emboss/emboss_fuzzpro.xml" />
<tool file="emboss/emboss_garnier.xml" />
<tool file="emboss/emboss_hmoment.xml" />
<tool file="emboss/emboss_iep.xml" />
<tool file="emboss/emboss_infoseq.xml" />
<tool file="emboss/emboss_maskfeat.xml" />
<tool file="emboss/emboss_maskseq.xml" />
<tool file="emboss/emboss_matcher.xml" />
<tool file="emboss/emboss_msbar.xml" />
<tool file="emboss/emboss_needle.xml" />
<tool file="emboss/emboss_newseq.xml" />
<tool file="emboss/emboss_noreturn.xml" />
<tool file="emboss/emboss_notseq.xml" />
<tool file="emboss/emboss_nthseq.xml" />
<tool file="emboss/emboss_octanol.xml" />
<tool file="emboss/emboss_oddcomp.xml" />
<tool file="emboss/emboss_pasteseq.xml" />
<tool file="emboss/emboss_patmatdb.xml" />
<tool file="emboss/emboss_pepcoil.xml" />
<tool file="emboss/emboss_pepinfo.xml" />
<tool file="emboss/emboss_pepstats.xml" />
<tool file="emboss/emboss_pepwheel.xml" />
<tool file="emboss/emboss_pepwindow.xml" />
<tool file="emboss/emboss_pepwindowall.xml" />
<tool file="emboss/emboss_polydot.xml" />
<tool file="emboss/emboss_seqmatchall.xml" />
<tool file="emboss/emboss_seqret.xml" />
<tool file="emboss/emboss_showfeat.xml" />
<tool file="emboss/emboss_shuffleseq.xml" />
<tool file="emboss/emboss_sigcleave.xml" />
<tool file="emboss/emboss_skipseq.xml" />
<tool file="emboss/emboss_splitter.xml" />
<tool file="emboss/emboss_stretcher.xml" />
<tool file="emboss/emboss_supermatcher.xml" />
<tool file="emboss/emboss_textsearch.xml" />
<tool file="emboss/emboss_tmap.xml" />
<tool file="emboss/emboss_tranalign.xml" />
<tool file="emboss/emboss_trimseq.xml" />
<tool file="emboss/emboss_twofeat.xml" />
<tool file="emboss/emboss_union.xml" />
<tool file="emboss/emboss_water.xml" />
<tool file="emboss/emboss_wordmatch.xml" />
</section>
-->
<!--
<section id="ePHYLIP" name="Run ePHYLIP">
<tool file="emboss/phylip/emboss_eclique.xml" />
<tool file="emboss/phylip/emboss_econsense.xml" />
<tool file="emboss/phylip/emboss_econtml.xml" />
<tool file="emboss/phylip/emboss_econtrast.xml" />
<tool file="emboss/phylip/emboss_ednacomp.xml" />
<tool file="emboss/phylip/emboss_ednadist.xml" />
<tool file="emboss/phylip/emboss_ednainvar.xml" />
<tool file="emboss/phylip/emboss_ednaml.xml" />
<tool file="emboss/phylip/emboss_ednamlk.xml" />
<tool file="emboss/phylip/emboss_ednapars.xml" />
<tool file="emboss/phylip/emboss_ednapenny.xml" />
<tool file="emboss/phylip/emboss_edollop.xml" />
<tool file="emboss/phylip/emboss_edolpenny.xml" />
<tool file="emboss/phylip/emboss_efactor.xml" />
<tool file="emboss/phylip/emboss_efitch.xml" />
<tool file="emboss/phylip/emboss_egendist.xml" />
<tool file="emboss/phylip/emboss_ekitsch.xml" />
<tool file="emboss/phylip/emboss_emix.xml" />
<tool file="emboss/phylip/emboss_eneighbor.xml" />
<tool file="emboss/phylip/emboss_epenny.xml" />
<tool file="emboss/phylip/emboss_eprotdist.xml" />
<tool file="emboss/phylip/emboss_eprotpars.xml" />
<tool file="emboss/phylip/emboss_erestml.xml" />
<tool file="emboss/phylip/emboss_eseqboot.xml" />
</section>
-->
<section name="PHYLIP" id="phylipnew">
<tool file="emboss/phylipnew/emboss_fdnadist.xml" />
<tool file="emboss/phylipnew/emboss_fdnapars.xml" />
<tool file="emboss/phylipnew/emboss_fdrawgram.xml" />
<tool file="emboss/phylipnew/emboss_ffitch.xml" />
<tool file="emboss/phylipnew/emboss_fseqboot.xml" />
<tool file="emboss/phylipnew/emboss_fneighbor.xml" />
<tool file="emboss/phylipnew/emboss_fprotdist.xml" />
<tool file="emboss/phylipnew/emboss_fprotpars.xml" />
</section>
<section name="HYPHY" id="hyphy">
<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
</section>
</toolbox>
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