commit/galaxy-central: kanwei: Standardize {datatypes|tool}_conf.xml.sample with 2 space indentation and newline before <label> blocks
1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e85c11175cdd/ changeset: e85c11175cdd user: kanwei date: 2011-10-05 05:29:08 summary: Standardize {datatypes|tool}_conf.xml.sample with 2 space indentation and newline before <label> blocks affected #: 2 files (-1 bytes) --- a/datatypes_conf.xml.sample Tue Oct 04 23:11:23 2011 -0400 +++ b/datatypes_conf.xml.sample Tue Oct 04 23:29:08 2011 -0400 @@ -1,352 +1,352 @@ <?xml version="1.0"?><datatypes> - <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> - <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/> - <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/> - <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> - <converter file="bam_to_bai.xml" target_datatype="bai"/> - <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/> - <display file="ucsc/bam.xml" /> - <display file="ensembl/ensembl_bam.xml" /> - <!-- <display file="igv/bam.xml" /> --> - </datatype> - <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"> - <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> - <converter file="interval_to_coverage.xml" target_datatype="coverage"/> - <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> - <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> - <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/> - <!-- <display file="ucsc/interval_as_bed.xml" /> --> - <display file="genetrack.xml" /> - </datatype> - <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" /> - <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /> - <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> - <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/> - </datatype> - <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /> - <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> - <converter file="len_to_linecount.xml" target_datatype="linecount" /> - </datatype> - <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true"> - <display file="ucsc/bigbed.xml" /> - </datatype> - <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true"> - <display file="ucsc/bigwig.xml" /> - </datatype> - <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> - <indexer file="coverage.xml" /> - </datatype> - <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> - <indexer file="coverage.xml" /> - </datatype> - <!-- MSI added Datatypes --> - <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /><!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' --> - <!-- End MSI added Datatypes --> - <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/> - <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/> - <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/> - <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/> - <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> - <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true"> - <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> - <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> - <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/> - <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> - <converter file="fasta_to_len.xml" target_datatype="len"/> - </datatype> - <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> - <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> - <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/> - <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/> - <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/> - <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/> - <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/> - <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> - <!-- <display file="genetrack.xml" /> --> - </datatype> - <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true"> - <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> - <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> - <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/> - <display file="ensembl/ensembl_gff.xml" inherit="True"/> - <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> --> - </datatype> - <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/> - <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/> - <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> - <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/> - <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/> - <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> - <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"> - <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> - <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/> - <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/> - <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/> - <indexer file="interval_awk.xml" /> - <!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> --> - <display file="genetrack.xml" inherit="True"/> - <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/> - <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> - </datatype> - <datatype extension="picard_interval_list" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> - <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> - <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> - <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> - <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> - <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/> - <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/> - <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/> - <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/> - <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/> - <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/> - <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/> - <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/> - <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/> - <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/> - <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/> - <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/> - <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> - <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/> - <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/> - <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> - <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/> - <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true"> - <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/> - <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> - </datatype> - <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack"> - <display file="ucsc/maf_customtrack.xml" /> - </datatype> - <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> - <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" /> - <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> - <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> - <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> - <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/> - <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> - <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> - <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/> - <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/> - <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> - <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> - <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> - <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> - <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> - <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/> - <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> - <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> - <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/> - <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"> - <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> - <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> - <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> - </datatype> - <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/> - <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> - <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"> - <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> - <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> - <!-- <display file="gbrowse/gbrowse_wig.xml" /> --> - </datatype> - <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" /> - <datatype extension="interval_index" type="galaxy.datatypes.data:Data" /> - <datatype extension="tabix" type="galaxy.datatypes.data:Data" /> - <datatype extension="bgzip" type="galaxy.datatypes.data:Data" /> - <!-- Start EMBOSS tools --> - <datatype extension="acedb" type="galaxy.datatypes.data:Text"/> - <datatype extension="asn1" type="galaxy.datatypes.data:Text"/> - <datatype extension="btwisted" type="galaxy.datatypes.data:Text"/> - <datatype extension="cai" type="galaxy.datatypes.data:Text"/> - <datatype extension="charge" type="galaxy.datatypes.data:Text"/> - <datatype extension="checktrans" type="galaxy.datatypes.data:Text"/> - <datatype extension="chips" type="galaxy.datatypes.data:Text"/> - <datatype extension="clustal" type="galaxy.datatypes.data:Text"/> - <datatype extension="codata" type="galaxy.datatypes.data:Text"/> - <datatype extension="codcmp" type="galaxy.datatypes.data:Text"/> - <datatype extension="coderet" type="galaxy.datatypes.data:Text"/> - <datatype extension="compseq" type="galaxy.datatypes.data:Text"/> - <datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/> - <datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/> - <datatype extension="cusp" type="galaxy.datatypes.data:Text"/> - <datatype extension="cut" type="galaxy.datatypes.data:Text"/> - <datatype extension="dan" type="galaxy.datatypes.data:Text"/> - <datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/> - <datatype extension="diffseq" type="galaxy.datatypes.data:Text"/> - <datatype extension="digest" type="galaxy.datatypes.data:Text"/> - <datatype extension="dreg" type="galaxy.datatypes.data:Text"/> - <datatype extension="einverted" type="galaxy.datatypes.data:Text"/> - <datatype extension="embl" type="galaxy.datatypes.data:Text"/> - <datatype extension="epestfind" type="galaxy.datatypes.data:Text"/> - <datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/> - <datatype extension="est2genome" type="galaxy.datatypes.data:Text"/> - <datatype extension="etandem" type="galaxy.datatypes.data:Text"/> - <datatype extension="excel" type="galaxy.datatypes.data:Text"/> - <datatype extension="feattable" type="galaxy.datatypes.data:Text"/> - <datatype extension="fitch" type="galaxy.datatypes.data:Text"/> - <datatype extension="freak" type="galaxy.datatypes.data:Text"/> - <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/> - <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/> - <datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/> - <datatype extension="garnier" type="galaxy.datatypes.data:Text"/> - <datatype extension="gcg" type="galaxy.datatypes.data:Text"/> - <datatype extension="geecee" type="galaxy.datatypes.data:Text"/> - <datatype extension="genbank" type="galaxy.datatypes.data:Text"/> - <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/> - <datatype extension="hennig86" type="galaxy.datatypes.data:Text"/> - <datatype extension="hmoment" type="galaxy.datatypes.data:Text"/> - <datatype extension="ig" type="galaxy.datatypes.data:Text"/> - <datatype extension="isochore" type="galaxy.datatypes.data:Text"/> - <datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/> - <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx10" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx1" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx0" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx3" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx2" type="galaxy.datatypes.data:Text"/> - <datatype extension="match" type="galaxy.datatypes.data:Text"/> - <datatype extension="mega" type="galaxy.datatypes.data:Text"/> - <datatype extension="meganon" type="galaxy.datatypes.data:Text"/> - <datatype extension="motif" type="galaxy.datatypes.data:Text"/> - <datatype extension="msf" type="galaxy.datatypes.data:Text"/> - <datatype extension="nametable" type="galaxy.datatypes.data:Text"/> - <datatype extension="ncbi" type="galaxy.datatypes.data:Text"/> - <datatype extension="needle" type="galaxy.datatypes.data:Text"/> - <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/> - <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/> - <datatype extension="nexus" type="galaxy.datatypes.data:Text"/> - <datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/> - <datatype extension="noreturn" type="galaxy.datatypes.data:Text"/> - <datatype extension="pair" type="galaxy.datatypes.data:Text"/> - <datatype extension="palindrome" type="galaxy.datatypes.data:Text"/> - <datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/> - <datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/> - <datatype extension="pepstats" type="galaxy.datatypes.data:Text"/> - <datatype extension="phylip" type="galaxy.datatypes.data:Text"/> - <datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/> - <datatype extension="pir" type="galaxy.datatypes.data:Text"/> - <datatype extension="polydot" type="galaxy.datatypes.data:Text"/> - <datatype extension="preg" type="galaxy.datatypes.data:Text"/> - <datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/> - <datatype extension="primersearch" type="galaxy.datatypes.data:Text"/> - <datatype extension="regions" type="galaxy.datatypes.data:Text"/> - <datatype extension="score" type="galaxy.datatypes.data:Text"/> - <datatype extension="selex" type="galaxy.datatypes.data:Text"/> - <datatype extension="seqtable" type="galaxy.datatypes.data:Text"/> - <datatype extension="showfeat" type="galaxy.datatypes.data:Text"/> - <datatype extension="showorf" type="galaxy.datatypes.data:Text"/> - <datatype extension="simple" type="galaxy.datatypes.data:Text"/> - <datatype extension="sixpack" type="galaxy.datatypes.data:Text"/> - <datatype extension="srs" type="galaxy.datatypes.data:Text"/> - <datatype extension="srspair" type="galaxy.datatypes.data:Text"/> - <datatype extension="staden" type="galaxy.datatypes.data:Text"/> - <datatype extension="strider" type="galaxy.datatypes.data:Text"/> - <datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/> - <datatype extension="swiss" type="galaxy.datatypes.data:Text"/> - <datatype extension="syco" type="galaxy.datatypes.data:Text"/> - <datatype extension="table" type="galaxy.datatypes.data:Text"/> - <datatype extension="textsearch" type="galaxy.datatypes.data:Text"/> - <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/> - <datatype extension="wobble" type="galaxy.datatypes.data:Text"/> - <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/> - <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/> - <!-- End EMBOSS tools --> - <!-- Start RGenetics Datatypes --> - <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> - <!-- eigenstrat pedigree input file --> - <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/> - <!-- eigenstrat pca output file for adjusted eigenQTL eg --> - <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/> - <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" /> - <!-- fbat/pbat format pedigree (header row of marker names) --> - <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/> - <!-- phenotype file - fbat format --> - <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/> - <!-- genome graphs ucsc file - first col is always marker then numeric values to plot --> - <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> - <!-- part of linkage format pedigree --> - <!-- information redundancy (LD) filtered plink pbed --> - <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true"> - </datatype> - <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> - <!-- linkage format pedigree (separate .map file) --> - <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> - <converter file="lped_to_fped_converter.xml" target_datatype="fped"/> - <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/> - </datatype> - <!-- plink compressed file - has bed extension unfortunately --> - <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> - <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> - <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/> - </datatype> - <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> - <!-- phenotype file - plink format --> - <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/> - <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/> - <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/> - <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/> - <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/> - <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> - <!-- End RGenetics Datatypes --> - </registration> - <sniffers> - <!-- - The order in which Galaxy attempts to determine data types is - important because some formats are much more loosely defined - than others. The following list should be the most rigidly - defined format first, followed by next-most rigidly defined, - and so on. - --> - <sniffer type="galaxy.datatypes.tabular:Vcf"/> - <sniffer type="galaxy.datatypes.binary:TwoBit"/> - <sniffer type="galaxy.datatypes.binary:Bam"/> - <sniffer type="galaxy.datatypes.binary:Sff"/> - <sniffer type="galaxy.datatypes.xml:BlastXml"/> - <sniffer type="galaxy.datatypes.sequence:Maf"/> - <sniffer type="galaxy.datatypes.sequence:Lav"/> - <sniffer type="galaxy.datatypes.sequence:csFasta"/> - <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> - <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> - <sniffer type="galaxy.datatypes.sequence:Fasta"/> - <sniffer type="galaxy.datatypes.sequence:Fastq"/> - <sniffer type="galaxy.datatypes.interval:Wiggle"/> - <sniffer type="galaxy.datatypes.images:Html"/> - <sniffer type="galaxy.datatypes.images:Pdf"/> - <sniffer type="galaxy.datatypes.sequence:Axt"/> - <sniffer type="galaxy.datatypes.interval:Bed"/> - <sniffer type="galaxy.datatypes.interval:CustomTrack"/> - <sniffer type="galaxy.datatypes.interval:Gtf"/> - <sniffer type="galaxy.datatypes.interval:Gff"/> - <sniffer type="galaxy.datatypes.interval:Gff3"/> - <sniffer type="galaxy.datatypes.tabular:Pileup"/> - <sniffer type="galaxy.datatypes.interval:Interval"/> - <sniffer type="galaxy.datatypes.tabular:Sam"/> - <sniffer type="galaxy.datatypes.images:Jpg"/> - <sniffer type="galaxy.datatypes.images:Png"/> - <sniffer type="galaxy.datatypes.images:Tiff"/> - <sniffer type="galaxy.datatypes.images:Bmp"/> - <sniffer type="galaxy.datatypes.images:Gif"/> - <sniffer type="galaxy.datatypes.images:Im"/> - <sniffer type="galaxy.datatypes.images:Pcd"/> - <sniffer type="galaxy.datatypes.images:Pcx"/> - <sniffer type="galaxy.datatypes.images:Ppm"/> - <sniffer type="galaxy.datatypes.images:Psd"/> - <sniffer type="galaxy.datatypes.images:Xbm"/> - <sniffer type="galaxy.datatypes.images:Xpm"/> - <sniffer type="galaxy.datatypes.images:Rgb"/> - <sniffer type="galaxy.datatypes.images:Pbm"/> - <sniffer type="galaxy.datatypes.images:Pgm"/> - <sniffer type="galaxy.datatypes.images:Xpm"/> - <sniffer type="galaxy.datatypes.images:Eps"/> - <sniffer type="galaxy.datatypes.images:Rast"/> - <!-- - Keep this commented until the sniff method in the assembly.py - module is fixed to not read the entire file. - <sniffer type="galaxy.datatypes.assembly:Amos"/> - --> - </sniffers> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/> + <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/> + <display file="ucsc/bam.xml" /> + <display file="ensembl/ensembl_bam.xml" /> + <!-- <display file="igv/bam.xml" /> --> + </datatype> + <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"> + <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> + <converter file="interval_to_coverage.xml" target_datatype="coverage"/> + <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <!-- <display file="ucsc/interval_as_bed.xml" /> --> + <display file="genetrack.xml" /> + </datatype> + <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" /> + <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /> + <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> + <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/> + </datatype> + <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /> + <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> + <converter file="len_to_linecount.xml" target_datatype="linecount" /> + </datatype> + <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigbed.xml" /> + </datatype> + <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true"> + <display file="ucsc/bigwig.xml" /> + </datatype> + <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> + <indexer file="coverage.xml" /> + </datatype> + <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> + <indexer file="coverage.xml" /> + </datatype> + <!-- MSI added Datatypes --> + <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /><!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' --> + <!-- End MSI added Datatypes --> + <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/> + <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/> + <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/> + <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true"> + <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> + <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> + <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/> + <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> + <converter file="fasta_to_len.xml" target_datatype="len"/> + </datatype> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/> + <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/> + <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/> + <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/> + <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> + <!-- <display file="genetrack.xml" /> --> + </datatype> + <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true"> + <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> + <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <display file="ensembl/ensembl_gff.xml" inherit="True"/> + <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> --> + </datatype> + <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/> + <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/> + <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> + <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/> + <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/> + <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> + <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"> + <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> + <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/> + <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/> + <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/> + <indexer file="interval_awk.xml" /> + <!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> --> + <display file="genetrack.xml" inherit="True"/> + <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/> + <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/> + </datatype> + <datatype extension="picard_interval_list" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> + <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/> + <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/> + <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/> + <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/> + <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/> + <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/> + <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/> + <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/> + <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/> + <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/> + <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/> + <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/> + <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> + <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/> + <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/> + <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> + <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/> + <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true"> + <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/> + <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> + </datatype> + <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack"> + <display file="ucsc/maf_customtrack.xml" /> + </datatype> + <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" /> + <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> + <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> + <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/> + <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> + <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> + <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/> + <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/> + <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> + <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> + <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> + <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/> + <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"> + <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + </datatype> + <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/> + <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> + <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"> + <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> + <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> + <!-- <display file="gbrowse/gbrowse_wig.xml" /> --> + </datatype> + <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" /> + <datatype extension="interval_index" type="galaxy.datatypes.data:Data" /> + <datatype extension="tabix" type="galaxy.datatypes.data:Data" /> + <datatype extension="bgzip" type="galaxy.datatypes.data:Data" /> + <!-- Start EMBOSS tools --> + <datatype extension="acedb" type="galaxy.datatypes.data:Text"/> + <datatype extension="asn1" type="galaxy.datatypes.data:Text"/> + <datatype extension="btwisted" type="galaxy.datatypes.data:Text"/> + <datatype extension="cai" type="galaxy.datatypes.data:Text"/> + <datatype extension="charge" type="galaxy.datatypes.data:Text"/> + <datatype extension="checktrans" type="galaxy.datatypes.data:Text"/> + <datatype extension="chips" type="galaxy.datatypes.data:Text"/> + <datatype extension="clustal" type="galaxy.datatypes.data:Text"/> + <datatype extension="codata" type="galaxy.datatypes.data:Text"/> + <datatype extension="codcmp" type="galaxy.datatypes.data:Text"/> + <datatype extension="coderet" type="galaxy.datatypes.data:Text"/> + <datatype extension="compseq" type="galaxy.datatypes.data:Text"/> + <datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/> + <datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/> + <datatype extension="cusp" type="galaxy.datatypes.data:Text"/> + <datatype extension="cut" type="galaxy.datatypes.data:Text"/> + <datatype extension="dan" type="galaxy.datatypes.data:Text"/> + <datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/> + <datatype extension="diffseq" type="galaxy.datatypes.data:Text"/> + <datatype extension="digest" type="galaxy.datatypes.data:Text"/> + <datatype extension="dreg" type="galaxy.datatypes.data:Text"/> + <datatype extension="einverted" type="galaxy.datatypes.data:Text"/> + <datatype extension="embl" type="galaxy.datatypes.data:Text"/> + <datatype extension="epestfind" type="galaxy.datatypes.data:Text"/> + <datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/> + <datatype extension="est2genome" type="galaxy.datatypes.data:Text"/> + <datatype extension="etandem" type="galaxy.datatypes.data:Text"/> + <datatype extension="excel" type="galaxy.datatypes.data:Text"/> + <datatype extension="feattable" type="galaxy.datatypes.data:Text"/> + <datatype extension="fitch" type="galaxy.datatypes.data:Text"/> + <datatype extension="freak" type="galaxy.datatypes.data:Text"/> + <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/> + <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/> + <datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/> + <datatype extension="garnier" type="galaxy.datatypes.data:Text"/> + <datatype extension="gcg" type="galaxy.datatypes.data:Text"/> + <datatype extension="geecee" type="galaxy.datatypes.data:Text"/> + <datatype extension="genbank" type="galaxy.datatypes.data:Text"/> + <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/> + <datatype extension="hennig86" type="galaxy.datatypes.data:Text"/> + <datatype extension="hmoment" type="galaxy.datatypes.data:Text"/> + <datatype extension="ig" type="galaxy.datatypes.data:Text"/> + <datatype extension="isochore" type="galaxy.datatypes.data:Text"/> + <datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/> + <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx10" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx1" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx0" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx3" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx2" type="galaxy.datatypes.data:Text"/> + <datatype extension="match" type="galaxy.datatypes.data:Text"/> + <datatype extension="mega" type="galaxy.datatypes.data:Text"/> + <datatype extension="meganon" type="galaxy.datatypes.data:Text"/> + <datatype extension="motif" type="galaxy.datatypes.data:Text"/> + <datatype extension="msf" type="galaxy.datatypes.data:Text"/> + <datatype extension="nametable" type="galaxy.datatypes.data:Text"/> + <datatype extension="ncbi" type="galaxy.datatypes.data:Text"/> + <datatype extension="needle" type="galaxy.datatypes.data:Text"/> + <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/> + <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/> + <datatype extension="nexus" type="galaxy.datatypes.data:Text"/> + <datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/> + <datatype extension="noreturn" type="galaxy.datatypes.data:Text"/> + <datatype extension="pair" type="galaxy.datatypes.data:Text"/> + <datatype extension="palindrome" type="galaxy.datatypes.data:Text"/> + <datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/> + <datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/> + <datatype extension="pepstats" type="galaxy.datatypes.data:Text"/> + <datatype extension="phylip" type="galaxy.datatypes.data:Text"/> + <datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/> + <datatype extension="pir" type="galaxy.datatypes.data:Text"/> + <datatype extension="polydot" type="galaxy.datatypes.data:Text"/> + <datatype extension="preg" type="galaxy.datatypes.data:Text"/> + <datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/> + <datatype extension="primersearch" type="galaxy.datatypes.data:Text"/> + <datatype extension="regions" type="galaxy.datatypes.data:Text"/> + <datatype extension="score" type="galaxy.datatypes.data:Text"/> + <datatype extension="selex" type="galaxy.datatypes.data:Text"/> + <datatype extension="seqtable" type="galaxy.datatypes.data:Text"/> + <datatype extension="showfeat" type="galaxy.datatypes.data:Text"/> + <datatype extension="showorf" type="galaxy.datatypes.data:Text"/> + <datatype extension="simple" type="galaxy.datatypes.data:Text"/> + <datatype extension="sixpack" type="galaxy.datatypes.data:Text"/> + <datatype extension="srs" type="galaxy.datatypes.data:Text"/> + <datatype extension="srspair" type="galaxy.datatypes.data:Text"/> + <datatype extension="staden" type="galaxy.datatypes.data:Text"/> + <datatype extension="strider" type="galaxy.datatypes.data:Text"/> + <datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/> + <datatype extension="swiss" type="galaxy.datatypes.data:Text"/> + <datatype extension="syco" type="galaxy.datatypes.data:Text"/> + <datatype extension="table" type="galaxy.datatypes.data:Text"/> + <datatype extension="textsearch" type="galaxy.datatypes.data:Text"/> + <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/> + <datatype extension="wobble" type="galaxy.datatypes.data:Text"/> + <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/> + <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/> + <!-- End EMBOSS tools --> + <!-- Start RGenetics Datatypes --> + <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> + <!-- eigenstrat pedigree input file --> + <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/> + <!-- eigenstrat pca output file for adjusted eigenQTL eg --> + <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/> + <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" /> + <!-- fbat/pbat format pedigree (header row of marker names) --> + <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/> + <!-- phenotype file - fbat format --> + <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/> + <!-- genome graphs ucsc file - first col is always marker then numeric values to plot --> + <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> + <!-- part of linkage format pedigree --> + <!-- information redundancy (LD) filtered plink pbed --> + <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true"> + </datatype> + <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> + <!-- linkage format pedigree (separate .map file) --> + <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> + <converter file="lped_to_fped_converter.xml" target_datatype="fped"/> + <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/> + </datatype> + <!-- plink compressed file - has bed extension unfortunately --> + <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> + <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> + <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/> + </datatype> + <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> + <!-- phenotype file - plink format --> + <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/> + <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/> + <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/> + <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/> + <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/> + <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> + <!-- End RGenetics Datatypes --> + </registration> + <sniffers> + <!-- + The order in which Galaxy attempts to determine data types is + important because some formats are much more loosely defined + than others. The following list should be the most rigidly + defined format first, followed by next-most rigidly defined, + and so on. + --> + <sniffer type="galaxy.datatypes.tabular:Vcf"/> + <sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:Bam"/> + <sniffer type="galaxy.datatypes.binary:Sff"/> + <sniffer type="galaxy.datatypes.xml:BlastXml"/> + <sniffer type="galaxy.datatypes.sequence:Maf"/> + <sniffer type="galaxy.datatypes.sequence:Lav"/> + <sniffer type="galaxy.datatypes.sequence:csFasta"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> + <sniffer type="galaxy.datatypes.sequence:Fasta"/> + <sniffer type="galaxy.datatypes.sequence:Fastq"/> + <sniffer type="galaxy.datatypes.interval:Wiggle"/> + <sniffer type="galaxy.datatypes.images:Html"/> + <sniffer type="galaxy.datatypes.images:Pdf"/> + <sniffer type="galaxy.datatypes.sequence:Axt"/> + <sniffer type="galaxy.datatypes.interval:Bed"/> + <sniffer type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer type="galaxy.datatypes.interval:Gtf"/> + <sniffer type="galaxy.datatypes.interval:Gff"/> + <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.tabular:Pileup"/> + <sniffer type="galaxy.datatypes.interval:Interval"/> + <sniffer type="galaxy.datatypes.tabular:Sam"/> + <sniffer type="galaxy.datatypes.images:Jpg"/> + <sniffer type="galaxy.datatypes.images:Png"/> + <sniffer type="galaxy.datatypes.images:Tiff"/> + <sniffer type="galaxy.datatypes.images:Bmp"/> + <sniffer type="galaxy.datatypes.images:Gif"/> + <sniffer type="galaxy.datatypes.images:Im"/> + <sniffer type="galaxy.datatypes.images:Pcd"/> + <sniffer type="galaxy.datatypes.images:Pcx"/> + <sniffer type="galaxy.datatypes.images:Ppm"/> + <sniffer type="galaxy.datatypes.images:Psd"/> + <sniffer type="galaxy.datatypes.images:Xbm"/> + <sniffer type="galaxy.datatypes.images:Xpm"/> + <sniffer type="galaxy.datatypes.images:Rgb"/> + <sniffer type="galaxy.datatypes.images:Pbm"/> + <sniffer type="galaxy.datatypes.images:Pgm"/> + <sniffer type="galaxy.datatypes.images:Xpm"/> + <sniffer type="galaxy.datatypes.images:Eps"/> + <sniffer type="galaxy.datatypes.images:Rast"/> + <!-- + Keep this commented until the sniff method in the assembly.py + module is fixed to not read the entire file. + <sniffer type="galaxy.datatypes.assembly:Amos"/> + --> + </sniffers></datatypes> --- a/tool_conf.xml.sample Tue Oct 04 23:11:23 2011 -0400 +++ b/tool_conf.xml.sample Tue Oct 04 23:29:08 2011 -0400 @@ -64,11 +64,12 @@ <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" /> + <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" /> @@ -144,8 +145,9 @@ <tool file="stats/plot_from_lda.xml" /><tool file="regVariation/t_test_two_samples.xml" /><tool file="regVariation/compute_q_values.xml" /> + <label text="GFF" id="gff" /> - <tool file="stats/count_gff_features.xml" /> + <tool file="stats/count_gff_features.xml" /></section><section name="Wavelet Analysis" id="dwt"><tool file="discreteWavelet/execute_dwt_var_perFeature.xml" /> @@ -156,7 +158,7 @@ <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /><tool file="discreteWavelet/execute_dwt_var_perClass.xml" /> --> - </section> + </section><section name="Graph/Display Data" id="plots"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" /> @@ -200,14 +202,14 @@ <tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section name="Evolution" id="hyphy"> + <section name="Evolution" id="hyphy"><tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /><tool file="hyphy/hyphy_nj_tree_wrapper.xml" /><tool file="hyphy/hyphy_dnds_wrapper.xml" /><tool file="evolution/mutate_snp_codon.xml" /><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /> - </section> + </section><section name="Motif Tools" id="motifs"><tool file="meme/meme.xml"/><tool file="meme/fimo.xml"/> @@ -216,7 +218,7 @@ <section name="Multiple Alignments" id="clustal"><tool file="rgenetics/rgClustalw.xml" /></section> - <section name="Metagenomic analyses" id="tax_manipulation"> + <section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /><tool file="taxonomy/t2ps_wrapper.xml" /> @@ -235,30 +237,35 @@ <tool file="fastx_toolkit/fastx_collapser.xml" /></section><section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> - <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> - <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /></section><section name="NGS: QC and manipulation" id="NGS_QC"> - <label text="FastQC: fastq/sam/bam" id="fastqcsambam" /> + + <label text="FastQC: fastq/sam/bam" id="fastqcsambam" /><tool file="rgenetics/rgFastQC.xml" /> - <label text="Illumina fastq" id="illumina" /> + + <label text="Illumina fastq" id="illumina" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" /><tool file="fastq/fastq_paired_end_joiner.xml" /><tool file="fastq/fastq_stats.xml" /> - <label text="Roche-454 data" id="454" /> + + <label text="Roche-454 data" id="454" /><tool file="metag_tools/short_reads_figure_score.xml" /><tool file="metag_tools/short_reads_trim_seq.xml" /><tool file="fastq/fastq_combiner.xml" /> - <label text="AB-SOLiD data" id="solid" /> + + <label text="AB-SOLiD data" id="solid" /><tool file="next_gen_conversion/solid2fastq.xml" /><tool file="solid_tools/solid_qual_stats.xml" /><tool file="solid_tools/solid_qual_boxplot.xml" /> - <label text="Generic FASTQ manipulation" id="generic_fastq" /> + + <label text="Generic FASTQ manipulation" id="generic_fastq" /><tool file="fastq/fastq_filter.xml" /><tool file="fastq/fastq_trimmer.xml" /><tool file="fastq/fastq_trimmer_by_quality.xml" /> @@ -269,7 +276,8 @@ <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> - <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /> + + <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /><tool file="fastx_toolkit/fastq_quality_converter.xml" /><tool file="fastx_toolkit/fastx_quality_statistics.xml" /><tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> @@ -283,9 +291,10 @@ <tool file="fastx_toolkit/fastx_collapser.xml" /><tool file="fastx_toolkit/fastx_renamer.xml" /><tool file="fastx_toolkit/fastx_reverse_complement.xml" /> - <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <tool file="fastx_toolkit/fastx_trimmer.xml" /></section><section name="NGS: Picard (beta)" id="picard_beta"> + <label text="QC/Metrics for sam/bam" id="qcsambam"/><tool file="picard/picard_BamIndexStats.xml" /><tool file="picard/rgPicardASMetrics.xml" /> @@ -293,7 +302,8 @@ <tool file="picard/rgPicardLibComplexity.xml" /><tool file="picard/rgPicardInsertSize.xml" /><tool file="picard/rgPicardHsMetrics.xml" /> - <label text="bam/sam Cleaning" id="picard-clean" /> + + <label text="bam/sam Cleaning" id="picard-clean" /><tool file="picard/picard_AddOrReplaceReadGroups.xml" /><tool file="picard/picard_ReorderSam.xml" /><tool file="picard/picard_ReplaceSamHeader.xml" /> @@ -306,108 +316,122 @@ included in the distribution but will not be hosted on our public servers for the current time. <section name="NGS: Assembly" id="ngs_assembly"> - <label text="Velvet" id="velvet"/> - <tool file="sr_assembly/velvetg.xml" /> - <tool file="sr_assembly/velveth.xml" /> + <label text="Velvet" id="velvet"/> + <tool file="sr_assembly/velvetg.xml" /> + <tool file="sr_assembly/velveth.xml" /></section> --><section name="NGS: Mapping" id="solexa_tools"> - <tool file="sr_mapping/lastz_wrapper.xml" /> - <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" /> - <tool file="sr_mapping/bowtie_wrapper.xml" /> - <tool file="sr_mapping/bowtie_color_wrapper.xml" /> - <tool file="sr_mapping/bwa_wrapper.xml" /> - <tool file="sr_mapping/bwa_color_wrapper.xml" /> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="metag_tools/megablast_wrapper.xml" /> - <tool file="metag_tools/megablast_xml_parser.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml"/> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bowtie_color_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> + <tool file="sr_mapping/bwa_color_wrapper.xml" /> + <tool file="sr_mapping/bfast_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <tool file="sr_mapping/PerM.xml" /> + <tool file="sr_mapping/srma_wrapper.xml" /> + <tool file="sr_mapping/mosaik.xml"/></section><section name="NGS: Indel Analysis" id="indel_analysis"> - <tool file="indels/sam_indel_filter.xml" /> - <tool file="indels/indel_sam2interval.xml" /> - <tool file="indels/indel_table.xml" /> - <tool file="indels/indel_analysis.xml" /> + <tool file="indels/sam_indel_filter.xml" /> + <tool file="indels/indel_sam2interval.xml" /> + <tool file="indels/indel_table.xml" /> + <tool file="indels/indel_analysis.xml" /></section><section name="NGS: RNA Analysis" id="ngs-rna-tools"> - <label text="RNA-seq" id="rna_seq" /> - <tool file="ngs_rna/tophat_wrapper.xml" /> - <tool file="ngs_rna/tophat_color_wrapper.xml" /> - <tool file="ngs_rna/cufflinks_wrapper.xml" /> - <tool file="ngs_rna/cuffcompare_wrapper.xml" /> - <tool file="ngs_rna/cuffdiff_wrapper.xml" /> - <!-- Trinity is very memory-intensive and should only be enabled/run - on instances with sufficient resources. - <label text="De novo Assembly" id="de_novo_assembly "/> - <tool file="ngs_rna/trinity_all.xml" /> - --> - <label text="Filtering" id="filtering" /> - <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> + + <label text="RNA-seq" id="rna_seq" /> + <tool file="ngs_rna/tophat_wrapper.xml" /> + <tool file="ngs_rna/tophat_color_wrapper.xml" /> + <tool file="ngs_rna/cufflinks_wrapper.xml" /> + <tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <!-- Trinity is very memory-intensive and should only be enabled/run + on instances with sufficient resources. + <label text="De novo Assembly" id="de_novo_assembly "/> + <tool file="ngs_rna/trinity_all.xml" /> + --> + + <label text="Filtering" id="filtering" /> + <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section><section name="NGS: SAM Tools" id="samtools"> - <tool file="samtools/sam_bitwise_flag_filter.xml" /> - <tool file="samtools/sam2interval.xml" /> - <tool file="samtools/sam_to_bam.xml" /> - <tool file="samtools/bam_to_sam.xml" /> - <tool file="samtools/sam_merge.xml" /> - <tool file="samtools/sam_pileup.xml" /> - <tool file="samtools/pileup_parser.xml" /> - <tool file="samtools/pileup_interval.xml" /> - <tool file="samtools/samtools_flagstat.xml" /> - <tool file="samtools/samtools_rmdup.xml" /> + <tool file="samtools/sam_bitwise_flag_filter.xml" /> + <tool file="samtools/sam2interval.xml" /> + <tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/bam_to_sam.xml" /> + <tool file="samtools/sam_merge.xml" /> + <tool file="samtools/sam_pileup.xml" /> + <tool file="samtools/pileup_parser.xml" /> + <tool file="samtools/pileup_interval.xml" /> + <tool file="samtools/samtools_flagstat.xml" /> + <tool file="samtools/samtools_rmdup.xml" /></section><section name="NGS: GATK Tools (beta)" id="gatk"> - <label text="Realignment" id="gatk_realignment" /> - <tool file="gatk/realigner_target_creator.xml" /> - <tool file="gatk/indel_realigner.xml" /> - <label text="Base Recalibration" id="gatk_recalibration" /> - <tool file="gatk/count_covariates.xml" /> - <tool file="gatk/table_recalibration.xml" /> - <tool file="gatk/analyze_covariates.xml" /> - <label text="Genotyping" id="gatk_genotyping" /> - <tool file="gatk/unified_genotyper.xml" /> - <label text="Annotation" id="gatk_annotation" /> - <tool file="gatk/variant_annotator.xml" /> - <label text="Filtration" id="gatk_filtration" /> - <tool file="gatk/variant_filtration.xml" /> - <tool file="gatk/variant_filtration.xml" /> - <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> - <tool file="gatk/variant_recalibrator.xml" /> - <tool file="gatk/variant_apply_recalibration.xml" /> - <label text="Variant Utilities" id="gatk_variant_utilities"/> - <tool file="gatk/variants_validate.xml" /> - <tool file="gatk/variant_eval.xml" /> - <tool file="gatk/variant_combine.xml" /> + + <label text="Realignment" id="gatk_realignment" /> + <tool file="gatk/realigner_target_creator.xml" /> + <tool file="gatk/indel_realigner.xml" /> + + <label text="Base Recalibration" id="gatk_recalibration" /> + <tool file="gatk/count_covariates.xml" /> + <tool file="gatk/table_recalibration.xml" /> + <tool file="gatk/analyze_covariates.xml" /> + + <label text="Genotyping" id="gatk_genotyping" /> + <tool file="gatk/unified_genotyper.xml" /> + + <label text="Annotation" id="gatk_annotation" /> + <tool file="gatk/variant_annotator.xml" /> + + <label text="Filtration" id="gatk_filtration" /> + <tool file="gatk/variant_filtration.xml" /> + <tool file="gatk/variant_filtration.xml" /> + + <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> + <tool file="gatk/variant_recalibrator.xml" /> + <tool file="gatk/variant_apply_recalibration.xml" /> + + <label text="Variant Utilities" id="gatk_variant_utilities"/> + <tool file="gatk/variants_validate.xml" /> + <tool file="gatk/variant_eval.xml" /> + <tool file="gatk/variant_combine.xml" /></section><section name="NGS: Peak Calling" id="peak_calling"> - <tool file="peak_calling/macs_wrapper.xml" /> - <tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="peak_calling/sicer_wrapper.xml" /> + <tool file="peak_calling/ccat_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /></section><section name="SNP/WGA: Data; Filters" id="rgdat"> - <label text="Data: Import and upload" id="rgimport" /> + + <label text="Data: Import and upload" id="rgimport" /><tool file="data_source/upload.xml"/><tool file="data_source/access_libraries.xml" /> - <label text="Data: Filter and Clean" id="rgfilter" /> + + <label text="Data: Filter and Clean" id="rgfilter" /><tool file="rgenetics/rgClean.xml"/><tool file="rgenetics/rgPedSub.xml"/><tool file="rgenetics/rgLDIndep.xml"/> - <label text="Simulate" id="rgsim" /> + + <label text="Simulate" id="rgsim" /><tool file="rgenetics/rgfakePhe.xml"/><tool file="rgenetics/rgfakePed.xml"/></section><section name="SNP/WGA: QC; LD; Plots" id="rgqcplot"> - <label text="QC; Eigenstrat" id="rgvisual" /> + + <label text="QC; Eigenstrat" id="rgvisual" /><tool file="rgenetics/rgQC.xml"/><tool file="rgenetics/rgEigPCA.xml"/> - <label text="LD; Manhattan/QQ; GRR" id="rgld" /> + + <label text="LD; Manhattan/QQ; GRR" id="rgld" /><tool file="rgenetics/rgHaploView.xml"/><tool file="rgenetics/rgManQQ.xml"/><tool file="rgenetics/rgGRR.xml"/> @@ -451,128 +475,128 @@ <tool file="ilmn_pacbio/quake.xml"/><tool file="ilmn_pacbio/quake_pe.xml"/><tool file="ilmn_pacbio/soap_denovo.xml"/> -<!-- + <!-- Uncomment this tool when we support the HDF5 format <tool file="ilmn_pacbio/smrtpipe_filter.xml"/> ---> + --><tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/><tool file="ilmn_pacbio/assembly_stats.xml"/></section> -<!-- + <!-- TODO: uncomment the following EMBOSS section whenever moving to test, but comment it in .sample to eliminate it from buildbot functional tests since these tools rarely change. ---> -<!-- + --> + <!-- <section name="EMBOSS" id="EMBOSSLite"> - <tool file="emboss_5/emboss_antigenic.xml" /> - <tool file="emboss_5/emboss_backtranseq.xml" /> - <tool file="emboss_5/emboss_banana.xml" /> - <tool file="emboss_5/emboss_biosed.xml" /> - <tool file="emboss_5/emboss_btwisted.xml" /> - <tool file="emboss_5/emboss_cai_custom.xml" /> - <tool file="emboss_5/emboss_cai.xml" /> - <tool file="emboss_5/emboss_chaos.xml" /> - <tool file="emboss_5/emboss_charge.xml" /> - <tool file="emboss_5/emboss_checktrans.xml" /> - <tool file="emboss_5/emboss_chips.xml" /> - <tool file="emboss_5/emboss_cirdna.xml" /> - <tool file="emboss_5/emboss_codcmp.xml" /> - <tool file="emboss_5/emboss_coderet.xml" /> - <tool file="emboss_5/emboss_compseq.xml" /> - <tool file="emboss_5/emboss_cpgplot.xml" /> - <tool file="emboss_5/emboss_cpgreport.xml" /> - <tool file="emboss_5/emboss_cusp.xml" /> - <tool file="emboss_5/emboss_cutseq.xml" /> - <tool file="emboss_5/emboss_dan.xml" /> - <tool file="emboss_5/emboss_degapseq.xml" /> - <tool file="emboss_5/emboss_descseq.xml" /> - <tool file="emboss_5/emboss_diffseq.xml" /> - <tool file="emboss_5/emboss_digest.xml" /> - <tool file="emboss_5/emboss_dotmatcher.xml" /> - <tool file="emboss_5/emboss_dotpath.xml" /> - <tool file="emboss_5/emboss_dottup.xml" /> - <tool file="emboss_5/emboss_dreg.xml" /> - <tool file="emboss_5/emboss_einverted.xml" /> - <tool file="emboss_5/emboss_epestfind.xml" /> - <tool file="emboss_5/emboss_equicktandem.xml" /> - <tool file="emboss_5/emboss_est2genome.xml" /> - <tool file="emboss_5/emboss_etandem.xml" /> - <tool file="emboss_5/emboss_extractfeat.xml" /> - <tool file="emboss_5/emboss_extractseq.xml" /> - <tool file="emboss_5/emboss_freak.xml" /> - <tool file="emboss_5/emboss_fuzznuc.xml" /> - <tool file="emboss_5/emboss_fuzzpro.xml" /> - <tool file="emboss_5/emboss_fuzztran.xml" /> - <tool file="emboss_5/emboss_garnier.xml" /> - <tool file="emboss_5/emboss_geecee.xml" /> - <tool file="emboss_5/emboss_getorf.xml" /> - <tool file="emboss_5/emboss_helixturnhelix.xml" /> - <tool file="emboss_5/emboss_hmoment.xml" /> - <tool file="emboss_5/emboss_iep.xml" /> - <tool file="emboss_5/emboss_infoseq.xml" /> - <tool file="emboss_5/emboss_isochore.xml" /> - <tool file="emboss_5/emboss_lindna.xml" /> - <tool file="emboss_5/emboss_marscan.xml" /> - <tool file="emboss_5/emboss_maskfeat.xml" /> - <tool file="emboss_5/emboss_maskseq.xml" /> - <tool file="emboss_5/emboss_matcher.xml" /> - <tool file="emboss_5/emboss_megamerger.xml" /> - <tool file="emboss_5/emboss_merger.xml" /> - <tool file="emboss_5/emboss_msbar.xml" /> - <tool file="emboss_5/emboss_needle.xml" /> - <tool file="emboss_5/emboss_newcpgreport.xml" /> - <tool file="emboss_5/emboss_newcpgseek.xml" /> - <tool file="emboss_5/emboss_newseq.xml" /> - <tool file="emboss_5/emboss_noreturn.xml" /> - <tool file="emboss_5/emboss_notseq.xml" /> - <tool file="emboss_5/emboss_nthseq.xml" /> - <tool file="emboss_5/emboss_octanol.xml" /> - <tool file="emboss_5/emboss_oddcomp.xml" /> - <tool file="emboss_5/emboss_palindrome.xml" /> - <tool file="emboss_5/emboss_pasteseq.xml" /> - <tool file="emboss_5/emboss_patmatdb.xml" /> - <tool file="emboss_5/emboss_pepcoil.xml" /> - <tool file="emboss_5/emboss_pepinfo.xml" /> - <tool file="emboss_5/emboss_pepnet.xml" /> - <tool file="emboss_5/emboss_pepstats.xml" /> - <tool file="emboss_5/emboss_pepwheel.xml" /> - <tool file="emboss_5/emboss_pepwindow.xml" /> - <tool file="emboss_5/emboss_pepwindowall.xml" /> - <tool file="emboss_5/emboss_plotcon.xml" /> - <tool file="emboss_5/emboss_plotorf.xml" /> - <tool file="emboss_5/emboss_polydot.xml" /> - <tool file="emboss_5/emboss_preg.xml" /> - <tool file="emboss_5/emboss_prettyplot.xml" /> - <tool file="emboss_5/emboss_prettyseq.xml" /> - <tool file="emboss_5/emboss_primersearch.xml" /> - <tool file="emboss_5/emboss_revseq.xml" /> - <tool file="emboss_5/emboss_seqmatchall.xml" /> - <tool file="emboss_5/emboss_seqret.xml" /> - <tool file="emboss_5/emboss_showfeat.xml" /> - <tool file="emboss_5/emboss_shuffleseq.xml" /> - <tool file="emboss_5/emboss_sigcleave.xml" /> - <tool file="emboss_5/emboss_sirna.xml" /> - <tool file="emboss_5/emboss_sixpack.xml" /> - <tool file="emboss_5/emboss_skipseq.xml" /> - <tool file="emboss_5/emboss_splitter.xml" /> - <tool file="emboss_5/emboss_supermatcher.xml" /> - <tool file="emboss_5/emboss_syco.xml" /> - <tool file="emboss_5/emboss_tcode.xml" /> - <tool 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file="emboss_5/emboss_charge.xml" /> + <tool file="emboss_5/emboss_checktrans.xml" /> + <tool file="emboss_5/emboss_chips.xml" /> + <tool file="emboss_5/emboss_cirdna.xml" /> + <tool file="emboss_5/emboss_codcmp.xml" /> + <tool file="emboss_5/emboss_coderet.xml" /> + <tool file="emboss_5/emboss_compseq.xml" /> + <tool file="emboss_5/emboss_cpgplot.xml" /> + <tool file="emboss_5/emboss_cpgreport.xml" /> + <tool file="emboss_5/emboss_cusp.xml" /> + <tool file="emboss_5/emboss_cutseq.xml" /> + <tool file="emboss_5/emboss_dan.xml" /> + <tool file="emboss_5/emboss_degapseq.xml" /> + <tool file="emboss_5/emboss_descseq.xml" /> + <tool file="emboss_5/emboss_diffseq.xml" /> + <tool file="emboss_5/emboss_digest.xml" /> + <tool file="emboss_5/emboss_dotmatcher.xml" /> + <tool file="emboss_5/emboss_dotpath.xml" /> + <tool file="emboss_5/emboss_dottup.xml" /> + <tool file="emboss_5/emboss_dreg.xml" /> + <tool file="emboss_5/emboss_einverted.xml" /> + <tool file="emboss_5/emboss_epestfind.xml" /> + <tool file="emboss_5/emboss_equicktandem.xml" /> + <tool file="emboss_5/emboss_est2genome.xml" /> + <tool file="emboss_5/emboss_etandem.xml" /> + <tool file="emboss_5/emboss_extractfeat.xml" /> + <tool file="emboss_5/emboss_extractseq.xml" /> + <tool file="emboss_5/emboss_freak.xml" /> + <tool file="emboss_5/emboss_fuzznuc.xml" /> + <tool file="emboss_5/emboss_fuzzpro.xml" /> + <tool file="emboss_5/emboss_fuzztran.xml" /> + <tool file="emboss_5/emboss_garnier.xml" /> + <tool file="emboss_5/emboss_geecee.xml" /> + <tool file="emboss_5/emboss_getorf.xml" /> + <tool file="emboss_5/emboss_helixturnhelix.xml" /> + <tool file="emboss_5/emboss_hmoment.xml" /> + <tool file="emboss_5/emboss_iep.xml" /> + <tool file="emboss_5/emboss_infoseq.xml" /> + <tool file="emboss_5/emboss_isochore.xml" /> + <tool file="emboss_5/emboss_lindna.xml" /> + <tool file="emboss_5/emboss_marscan.xml" /> + <tool file="emboss_5/emboss_maskfeat.xml" /> + <tool file="emboss_5/emboss_maskseq.xml" /> + <tool file="emboss_5/emboss_matcher.xml" /> + <tool file="emboss_5/emboss_megamerger.xml" /> + <tool file="emboss_5/emboss_merger.xml" /> + <tool file="emboss_5/emboss_msbar.xml" /> + <tool file="emboss_5/emboss_needle.xml" /> + <tool file="emboss_5/emboss_newcpgreport.xml" /> + <tool file="emboss_5/emboss_newcpgseek.xml" /> + <tool file="emboss_5/emboss_newseq.xml" /> + <tool file="emboss_5/emboss_noreturn.xml" /> + <tool file="emboss_5/emboss_notseq.xml" /> + <tool file="emboss_5/emboss_nthseq.xml" /> + <tool file="emboss_5/emboss_octanol.xml" /> + <tool file="emboss_5/emboss_oddcomp.xml" /> + <tool file="emboss_5/emboss_palindrome.xml" /> + <tool file="emboss_5/emboss_pasteseq.xml" /> + <tool file="emboss_5/emboss_patmatdb.xml" /> + <tool file="emboss_5/emboss_pepcoil.xml" /> + <tool file="emboss_5/emboss_pepinfo.xml" /> + <tool file="emboss_5/emboss_pepnet.xml" /> + <tool file="emboss_5/emboss_pepstats.xml" /> + <tool file="emboss_5/emboss_pepwheel.xml" /> + <tool file="emboss_5/emboss_pepwindow.xml" /> + <tool file="emboss_5/emboss_pepwindowall.xml" /> + <tool file="emboss_5/emboss_plotcon.xml" /> + <tool file="emboss_5/emboss_plotorf.xml" /> + <tool file="emboss_5/emboss_polydot.xml" /> + <tool file="emboss_5/emboss_preg.xml" /> + <tool file="emboss_5/emboss_prettyplot.xml" /> + <tool file="emboss_5/emboss_prettyseq.xml" /> + <tool file="emboss_5/emboss_primersearch.xml" /> + <tool file="emboss_5/emboss_revseq.xml" /> + <tool file="emboss_5/emboss_seqmatchall.xml" /> + <tool file="emboss_5/emboss_seqret.xml" /> + <tool file="emboss_5/emboss_showfeat.xml" /> + <tool file="emboss_5/emboss_shuffleseq.xml" /> + <tool file="emboss_5/emboss_sigcleave.xml" /> + <tool file="emboss_5/emboss_sirna.xml" /> + <tool file="emboss_5/emboss_sixpack.xml" /> + <tool file="emboss_5/emboss_skipseq.xml" /> + <tool file="emboss_5/emboss_splitter.xml" /> + <tool file="emboss_5/emboss_supermatcher.xml" /> + <tool file="emboss_5/emboss_syco.xml" /> + <tool file="emboss_5/emboss_tcode.xml" /> + <tool file="emboss_5/emboss_textsearch.xml" /> + <tool file="emboss_5/emboss_tmap.xml" /> + <tool file="emboss_5/emboss_tranalign.xml" /> + <tool file="emboss_5/emboss_transeq.xml" /> + <tool file="emboss_5/emboss_trimest.xml" /> + <tool file="emboss_5/emboss_trimseq.xml" /> + <tool file="emboss_5/emboss_twofeat.xml" /> + <tool file="emboss_5/emboss_union.xml" /> + <tool file="emboss_5/emboss_vectorstrip.xml" /> + <tool file="emboss_5/emboss_water.xml" /> + <tool file="emboss_5/emboss_wobble.xml" /> + <tool file="emboss_5/emboss_wordcount.xml" /> + <tool file="emboss_5/emboss_wordmatch.xml" /></section> ---> + --></toolbox> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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