mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Wen-Yu Chung
9f0f822deb
tools for running phred(need to change path later), trim sequence, generate boxplot and an array of length of the reads. test data are added. trim sequence and array of length passed functional test. phred (2 ouput files) and boxplot (pdf file) didn't pass functional test yet.
304 lines
14 KiB
XML
304 lines
14 KiB
XML
<?xml version="1.0"?>
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<toolbox>
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<section name="Get Data" id="getext">
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<tool file="data_source/upload.xml"/>
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<tool file="data_source/ucsc_tablebrowser.xml" />
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<tool file="data_source/ucsc_tablebrowser_test.xml" />
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<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
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<tool file="data_source/microbial_import.xml" />
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<tool file="data_source/biomart.xml" />
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<tool file="data_source/biomart_test.xml" />
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<tool file="data_source/encode_db.xml" />
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<tool file="data_source/hbvar.xml" />
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<tool file="validation/fix_errors.xml" />
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</section>
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<section name="Get ENCODE Data" id="encode">
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<tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/>
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<tool file="data_source/encode_import_genes_and_transcripts.xml"/>
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<tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/>
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<tool file="data_source/encode_import_transcription_regulation.xml"/>
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<tool file="data_source/encode_import_all_latest_datasets.xml" />
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<tool file="data_source/encode_import_gencode.xml" />
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</section>
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<section name="ENCODE Tools" id="EncodeTools">
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<!-- <tool file="extract/interval2maf.xml" />
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<tool file="extract/phastOdds/phastOdds_tool.xml" />
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<tool file="stats/aggregate_binned_scores_in_intervals.xml" /> -->
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<tool file="encode/gencode_partition.xml" />
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<tool file="encode/random_intervals.xml" />
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</section>
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<section name="Text Manipulation" id="textutil">
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<tool file="filters/fixedValueColumn.xml" />
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<tool file="stats/column_maker.xml" />
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<tool file="filters/catWrapper.xml" />
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<tool file="filters/condense_characters.xml" />
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<tool file="filters/convert_characters.xml" />
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<tool file="filters/CreateInterval.xml" />
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<tool file="filters/cutWrapper.xml" />
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<tool file="filters/pasteWrapper.xml" />
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<tool file="filters/remove_beginning.xml" />
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<tool file="filters/headWrapper.xml" />
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<tool file="filters/tailWrapper.xml" />
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</section>
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<section name="Filter and Sort" id="filter">
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<tool file="stats/filtering.xml" />
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<tool file="filters/sorter.xml" />
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<tool file="filters/grep.xml" />
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</section>
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<section name="Join, Subtract and Group" id="group">
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<tool file="filters/joiner.xml" />
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<tool file="filters/compare.xml"/>
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<tool file="new_operations/subtract_query.xml"/>
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<tool file="stats/grouping.xml" />
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</section>
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<section name="Convert Formats" id="convert">
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<tool file="filters/maf/maf_to_fasta.xml" />
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<tool file="filters/maf/maf_to_bed.xml" />
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<tool file="filters/gff2bed.xml" />
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<tool file="filters/bed2gff.xml" />
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<tool file="filters/axt_to_fasta.xml" />
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<tool file="filters/axt_to_concat_fasta.xml" />
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<tool file="filters/axt_to_lav.xml" />
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<tool file="filters/lav_to_bed.xml" />
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</section>
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<section name="Extract Features" id="features">
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<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
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<tool file="extract/extract_GFF_Features.xml" />
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</section>
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<section name="Pattern-Matching" id="patmat">
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<tool file="patmat/findcluster_mysql.xml" />
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</section>
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<section name="Fetch Sequences" id="fetchSeq">
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<tool file="extract/fasta-subseq-wrapper.xml" />
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<tool file="extract/twoBitToFa_wrapper.xml" />
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</section>
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<section name="Fetch Alignments" id="fetchAlign">
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<tool file="extract/interval2maf_pairwise.xml" />
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<tool file="extract/interval2maf.xml" />
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<tool file="extract/interval_maf_to_merged_fasta.xml" />
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<tool file="extract/genebed_maf_to_fasta.xml"/>
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<tool file="filters/maf/maf_stats.xml"/>
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<tool file="filters/maf/maf_thread_for_species.xml"/>
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<tool file="filters/maf/maf_limit_to_species.xml"/>
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<tool file="filters/maf/maf_limit_size.xml"/>
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<tool file="filters/maf/maf_by_block_number.xml"/>
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<tool file="filters/maf/maf_reverse_complement.xml"/>
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<tool file="filters/maf/maf_filter.xml"/>
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</section>
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<section name="Get Genomic Scores" id="scores">
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<tool file="stats/wiggle_to_simple.xml" />
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<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
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<tool file="extract/phastOdds/phastOdds_tool.xml" />
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</section>
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<section name="Operate on Genomic Intervals" id="bxops">
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<tool file="new_operations/intersect.xml" id="intersect" />
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<tool file="new_operations/subtract.xml" id="subtract" />
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<tool file="new_operations/merge.xml" id="merge" />
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<tool file="new_operations/concat.xml" id="concat" />
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<tool file="new_operations/basecoverage.xml" id="basecoverage" />
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<tool file="new_operations/coverage.xml" id="coverage" />
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<tool file="new_operations/complement.xml" id="complement" />
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<tool file="new_operations/cluster.xml" id="cluster" />
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<tool file="new_operations/join.xml" id="join" />
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<tool file="new_operations/get_flanks.xml" />
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</section>
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<section name="Statistics" id="stats">
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<tool file="stats/gsummary.xml" />
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<tool file="filters/uniq.xml" />
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<tool file="stats/cor.xml" />
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</section>
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<section name="Graph/Display Data" id="plots">
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<tool file="plotting/histogram2.xml" />
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<tool file="plotting/scatterplot.xml" />
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<tool file="plotting/xy_plot.xml" />
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<tool file="visualization/GMAJ.xml" />
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<tool file="visualization/LAJ.xml" />
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<tool file="visualization/build_ucsc_custom_track.xml" />
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</section>
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<section name="Regional Variation" id="regVar">
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<tool file="regVariation/windowSplitter.xml" />
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<tool file="regVariation/featureCounter.xml" />
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<tool file="regVariation/quality_filter.xml" />
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<tool file="regVariation/maf_cpg_filter.xml" />
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<tool file="regVariation/getIndels_2way.xml" />
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<tool file="regVariation/getIndels_3way.xml" />
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</section>
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<section name="Evolution: HyPhy" id="hyphy">
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<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
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<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
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<tool file="hyphy/hyphy_dnds_wrapper.xml" />
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</section>
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<section name="EMBOSS" id="EMBOSSLite">
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<tool file="emboss/emboss_cai.xml" />
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<tool file="emboss/emboss_cai_custom.xml" />
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<!-- <tool file="emboss/emboss_codcmp.xml" /> -->
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<tool file="emboss/emboss_compseq.xml" />
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<!-- <tool file="emboss/emboss_cpgplot.xml" /> -->
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<tool file="emboss/emboss_cpgreport.xml" />
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<tool file="emboss/emboss_cusp.xml" />
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<tool file="emboss/emboss_cutseq.xml" />
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<!-- <tool file="emboss/emboss_dan.xml" /> -->
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<tool file="emboss/emboss_einverted.xml" />
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<tool file="emboss/emboss_equicktandem.xml" />
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<tool file="emboss/emboss_est2genome.xml" />
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<tool file="emboss/emboss_etandem.xml" />
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<!-- <tool file="emboss/emboss_freak.xml" /> -->
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<tool file="emboss/emboss_fuzznuc.xml" />
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<tool file="emboss/emboss_fuzztran.xml" />
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<tool file="emboss/emboss_getorf.xml" />
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<tool file="emboss/emboss_isochore.xml" />
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<tool file="emboss/emboss_msbar.xml" />
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<tool file="emboss/emboss_needle.xml" />
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<!-- <tool file="emboss/emboss_newcpgreport.xml" /> -->
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<tool file="emboss/emboss_newcpgseek.xml" />
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<tool file="emboss/emboss_newseq.xml" />
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<tool file="emboss/emboss_notseq.xml" />
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<tool file="emboss/emboss_nthseq.xml" />
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<tool file="emboss/emboss_palindrome.xml" />
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<tool file="emboss/emboss_pasteseq.xml" />
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<tool file="emboss/emboss_plotorf.xml" />
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<tool file="emboss/emboss_polydot.xml" />
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<tool file="emboss/emboss_prettyseq.xml" />
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<tool file="emboss/emboss_primersearch.xml" />
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<tool file="emboss/emboss_revseq.xml" />
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<tool file="emboss/emboss_seqmatchall.xml" />
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<!-- <tool file="emboss/emboss_showorf.xml" /> -->
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<tool file="emboss/emboss_shuffleseq.xml" />
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<tool file="emboss/emboss_sirna.xml" />
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<tool file="emboss/emboss_sixpack.xml" />
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<tool file="emboss/emboss_splitter.xml" />
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<!-- <tool file="emboss/emboss_stretcher.xml" /> -->
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<tool file="emboss/emboss_supermatcher.xml" />
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<tool file="emboss/emboss_syco.xml" />
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<tool file="emboss/emboss_tranalign.xml" />
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<tool file="emboss/emboss_transeq.xml" />
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<tool file="emboss/emboss_trimest.xml" />
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<tool file="emboss/emboss_trimseq.xml" />
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<tool file="emboss/emboss_union.xml" />
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<tool file="emboss/emboss_vectorstrip.xml" />
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<tool file="emboss/emboss_water.xml" />
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<tool file="emboss/emboss_wobble.xml" />
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<tool file="emboss/emboss_wordcount.xml" />
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<tool file="emboss/emboss_wordmatch.xml" />
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<tool file="emboss/emboss_backtranseq.xml" />
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<tool file="emboss/emboss_biosed.xml" />
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<tool file="emboss/emboss_charge.xml" />
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<tool file="emboss/emboss_checktrans.xml" />
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</section>
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<!-- <section name="EMBOSS_5" id="EMBOSSLite_5">
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<tool file="emboss_5/emboss_antigenic.xml" />
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<tool file="emboss_5/emboss_backtranseq.xml" />
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<tool file="emboss_5/emboss_banana.xml" />
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<tool file="emboss_5/emboss_btwisted.xml" />
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<tool file="emboss_5/emboss_biosed.xml" />
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<tool file="emboss_5/emboss_cai.xml" />
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<tool file="emboss_5/emboss_cai_custom.xml" />
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<tool file="emboss_5/emboss_chaos.xml" />
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<tool file="emboss_5/emboss_chips.xml" />
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<tool file="emboss_5/emboss_charge.xml" />
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<tool file="emboss_5/emboss_checktrans.xml" />
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<tool file="emboss_5/emboss_cirdna.xml" />
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<tool file="emboss_5/emboss_codcmp.xml" />
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<tool file="emboss_5/emboss_coderet.xml" />
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<tool file="emboss_5/emboss_compseq.xml" />
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<tool file="emboss_5/emboss_cpgplot.xml" />
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<tool file="emboss_5/emboss_cpgreport.xml" />
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<tool file="emboss_5/emboss_cusp.xml" />
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<tool file="emboss_5/emboss_cutseq.xml" />
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<tool file="emboss_5/emboss_dan.xml" />
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<tool file="emboss_5/emboss_degapseq.xml" />
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<tool file="emboss_5/emboss_descseq.xml" />
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<tool file="emboss_5/emboss_diffseq.xml" />
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<tool file="emboss_5/emboss_digest.xml" />
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<tool file="emboss_5/emboss_dotmatcher.xml" />
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<tool file="emboss_5/emboss_dotpath.xml" />
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<tool file="emboss_5/emboss_dottup.xml" />
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<tool file="emboss_5/emboss_dreg.xml" />
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<tool file="emboss_5/emboss_einverted.xml" />
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<tool file="emboss_5/emboss_epestfind.xml" />
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<tool file="emboss_5/emboss_equicktandem.xml" />
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<tool file="emboss_5/emboss_est2genome.xml" />
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<tool file="emboss_5/emboss_etandem.xml" />
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<tool file="emboss_5/emboss_extractfeat.xml" />
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<tool file="emboss_5/emboss_extractseq.xml" />
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<tool file="emboss_5/emboss_freak.xml" />
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<tool file="emboss_5/emboss_fuzznuc.xml" />
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<tool file="emboss_5/emboss_fuzztran.xml" />
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<tool file="emboss_5/emboss_fuzzpro.xml" />
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<tool file="emboss_5/emboss_garner.xml" />
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<tool file="emboss_5/emboss_geecee.xml" />
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<tool file="emboss_5/emboss_getorf.xml" />
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<tool file="emboss_5/emboss_helixturnhelix.xml" />
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<tool file="emboss_5/emboss_hmoment.xml" />
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<tool file="emboss_5/emboss_iep.xml" />
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<tool file="emboss_5/emboss_infoseq.xml" />
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<tool file="emboss_5/emboss_isochore.xml" />
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<tool file="emboss_5/emboss_lindna.xml" />
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<tool file="emboss_5/emboss_marscan.xml" />
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<tool file="emboss_5/emboss_maskfeat.xml" />
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<tool file="emboss_5/emboss_maskseq.xml" />
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<tool file="emboss_5/emboss_matcher.xml" />
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<tool file="emboss_5/emboss_megamerger.xml" />
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<tool file="emboss_5/emboss_merger.xml" />
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<tool file="emboss_5/emboss_msbar.xml" />
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<tool file="emboss_5/emboss_needle.xml" />
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<tool file="emboss_5/emboss_newcpgreport.xml" />
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<tool file="emboss_5/emboss_newcpgseek.xml" />
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<tool file="emboss_5/emboss_newseq.xml" />
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<tool file="emboss_5/emboss_notseq.xml" />
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<tool file="emboss_5/emboss_nthseq.xml" />
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<tool file="emboss_5/emboss_octanol.xml" />
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<tool file="emboss_5/emboss_oddcomp.xml" />
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<tool file="emboss_5/emboss_patmatdb.xml" />
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<tool file="emboss_5/emboss_palindrome.xml" />
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<tool file="emboss_5/emboss_pasteseq.xml" />
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<tool file="emboss_5/emboss_pepcoil.xml" />
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<tool file="emboss_5/emboss_pepinfo.xml" />
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<tool file="emboss_5/emboss_pepnet.xml" />
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<tool file="emboss_5/emboss_pepstats.xml" />
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<tool file="emboss_5/emboss_pepwheel.xml" />
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<tool file="emboss_5/emboss_pepwindow.xml" />
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<tool file="emboss_5/emboss_pepwindowall.xml" />
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<tool file="emboss_5/emboss_plotcon.xml" />
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<tool file="emboss_5/emboss_plotorf.xml" />
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<tool file="emboss_5/emboss_polydot.xml" />
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<tool file="emboss_5/emboss_preg.xml" />
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<tool file="emboss_5/emboss_prettyplot.xml" />
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<tool file="emboss_5/emboss_prettyseq.xml" />
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<tool file="emboss_5/emboss_primersearch.xml" />
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<tool file="emboss_5/emboss_revseq.xml" />
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<tool file="emboss_5/emboss_seqmatchall.xml" />
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<tool file="emboss_5/emboss_seqret.xml" />
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<tool file="emboss_5/emboss_showorf.xml" />
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<tool file="emboss_5/emboss_shuffleseq.xml" />
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<tool file="emboss_5/emboss_sigcleave.xml" />
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<tool file="emboss_5/emboss_sirna.xml" />
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<tool file="emboss_5/emboss_sixpack.xml" />
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<tool file="emboss_5/emboss_skipseq.xml" />
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<tool file="emboss_5/emboss_splitter.xml" />
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<tool file="emboss_5/emboss_supermatcher.xml" />
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<tool file="emboss_5/emboss_syco.xml" />
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<tool file="emboss_5/emboss_tcode.xml" />
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<tool file="emboss_5/emboss_textsearch.xml" />
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<tool file="emboss_5/emboss_tmap.xml" />
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<tool file="emboss_5/emboss_tranalign.xml" />
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<tool file="emboss_5/emboss_transeq.xml" />
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<tool file="emboss_5/emboss_trimest.xml" />
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<tool file="emboss_5/emboss_trimseq.xml" />
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<tool file="emboss_5/emboss_twofeat.xml" />
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<tool file="emboss_5/emboss_union.xml" />
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<tool file="emboss_5/emboss_vectorstrip.xml" />
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<tool file="emboss_5/emboss_water.xml" />
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<tool file="emboss_5/emboss_wobble.xml" />
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<tool file="emboss_5/emboss_wordcount.xml" />
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<tool file="emboss_5/emboss_wordmatch.xml" />
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</section> -->
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<section name="Metagenomics" id="metagenomics">
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<tool file="metag_tools/short_reads_run_phred.xml" />
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<tool file="metag_tools/short_reads_trim_seq.xml" />
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<tool file="metag_tools/short_reads_figure_score.xml" />
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<tool file="metag_tools/short_reads_figure_length.xml" />
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</section>
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</toolbox>
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