Mercurial > repos > erick-antezana > onto-toolkit

annotate onto-toolkit/datatypes_conf.xml @ 1:d2d26d330236

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v 0.2: tools added for OPPL-galaxy
author easr
date Wed, 11 Apr 2012 10:33:41 +0200
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1 <?xml version="1.0"?>
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2 <datatypes>
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3 <registration converters_path="lib/galaxy/datatypes/converters">
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4 <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
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5 <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
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6 <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">
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7 <converter file="bam_to_bai.xml" target_datatype="bai"/>
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8 </datatype>
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9 <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
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10 <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
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11 <converter file="interval_to_coverage.xml" target_datatype="coverage"/>
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12 <converter file="bed_to_interval_index_converter.xml" target_datatype="interval_index"/>
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13 </datatype>
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14 <datatype extension="binseq.zip" type="galaxy.datatypes.binary:Binseq" mimetype="application/zip" display_in_upload="true"/>
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15 <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
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16 <!-- no converters yet -->
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17 </datatype>
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18 <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
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19 <indexer file="coverage.xml" />
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20 </datatype>
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21 <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
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22 <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
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23 <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
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24 <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
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25 <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
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26 </datatype>
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27 <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/>
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28 <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/>
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29 <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/>
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30 <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
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31 <converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
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32 </datatype>
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33 <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
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34 <datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
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35 <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
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36 <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
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37 <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
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38 <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
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39 <indexer file="interval_awk.xml" />
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40 </datatype>
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41 <datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
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42 <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
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43 <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
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44 <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
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45 <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
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46 <converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
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47 </datatype>
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48 <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
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49 <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
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50 <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
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51 <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
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52 <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
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53 <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/>
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54 <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
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55 <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
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56 <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
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57 <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
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58 <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
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59 <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/>
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60 <datatype extension="txtseq.zip" type="galaxy.datatypes.data:Txtseq" mimetype="application/zip" display_in_upload="true"/>
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61 <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
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62 <converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/>
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63 <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
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64 </datatype>
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65 <datatype extension="array_tree" type="galaxy.datatypes.data:Data" />
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66 <datatype extension="interval_index" type="galaxy.datatypes.data:Data" />
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67 <!-- Start EMBOSS tools -->
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68 <datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
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69 <datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
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70 <datatype extension="btwisted" type="galaxy.datatypes.data:Text"/>
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71 <datatype extension="cai" type="galaxy.datatypes.data:Text"/>
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72 <datatype extension="charge" type="galaxy.datatypes.data:Text"/>
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73 <datatype extension="checktrans" type="galaxy.datatypes.data:Text"/>
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74 <datatype extension="chips" type="galaxy.datatypes.data:Text"/>
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75 <datatype extension="clustal" type="galaxy.datatypes.data:Text"/>
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76 <datatype extension="codata" type="galaxy.datatypes.data:Text"/>
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77 <datatype extension="codcmp" type="galaxy.datatypes.data:Text"/>
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78 <datatype extension="coderet" type="galaxy.datatypes.data:Text"/>
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79 <datatype extension="compseq" type="galaxy.datatypes.data:Text"/>
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80 <datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/>
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81 <datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/>
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82 <datatype extension="cusp" type="galaxy.datatypes.data:Text"/>
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83 <datatype extension="cut" type="galaxy.datatypes.data:Text"/>
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84 <datatype extension="dan" type="galaxy.datatypes.data:Text"/>
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85 <datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/>
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86 <datatype extension="diffseq" type="galaxy.datatypes.data:Text"/>
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87 <datatype extension="digest" type="galaxy.datatypes.data:Text"/>
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88 <datatype extension="dreg" type="galaxy.datatypes.data:Text"/>
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89 <datatype extension="einverted" type="galaxy.datatypes.data:Text"/>
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90 <datatype extension="embl" type="galaxy.datatypes.data:Text"/>
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91 <datatype extension="epestfind" type="galaxy.datatypes.data:Text"/>
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92 <datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/>
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93 <datatype extension="est2genome" type="galaxy.datatypes.data:Text"/>
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94 <datatype extension="etandem" type="galaxy.datatypes.data:Text"/>
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95 <datatype extension="excel" type="galaxy.datatypes.data:Text"/>
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96 <datatype extension="feattable" type="galaxy.datatypes.data:Text"/>
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97 <datatype extension="fitch" type="galaxy.datatypes.data:Text"/>
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98 <datatype extension="freak" type="galaxy.datatypes.data:Text"/>
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99 <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/>
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100 <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/>
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101 <datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/>
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102 <datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
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103 <datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
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104 <datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
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105 <datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
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106 <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
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107 <datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
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108 <datatype extension="hmoment" type="galaxy.datatypes.data:Text"/>
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109 <datatype extension="ig" type="galaxy.datatypes.data:Text"/>
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110 <datatype extension="isochore" type="galaxy.datatypes.data:Text"/>
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111 <datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/>
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112 <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/>
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113 <datatype extension="markx10" type="galaxy.datatypes.data:Text"/>
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114 <datatype extension="markx1" type="galaxy.datatypes.data:Text"/>
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115 <datatype extension="markx0" type="galaxy.datatypes.data:Text"/>
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116 <datatype extension="markx3" type="galaxy.datatypes.data:Text"/>
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117 <datatype extension="markx2" type="galaxy.datatypes.data:Text"/>
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118 <datatype extension="match" type="galaxy.datatypes.data:Text"/>
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119 <datatype extension="mega" type="galaxy.datatypes.data:Text"/>
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120 <datatype extension="meganon" type="galaxy.datatypes.data:Text"/>
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121 <datatype extension="motif" type="galaxy.datatypes.data:Text"/>
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122 <datatype extension="msf" type="galaxy.datatypes.data:Text"/>
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123 <datatype extension="nametable" type="galaxy.datatypes.data:Text"/>
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124 <datatype extension="ncbi" type="galaxy.datatypes.data:Text"/>
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125 <datatype extension="needle" type="galaxy.datatypes.data:Text"/>
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126 <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/>
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127 <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/>
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128 <datatype extension="nexus" type="galaxy.datatypes.data:Text"/>
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129 <datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/>
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130 <datatype extension="noreturn" type="galaxy.datatypes.data:Text"/>
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131 <datatype extension="pair" type="galaxy.datatypes.data:Text"/>
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132 <datatype extension="palindrome" type="galaxy.datatypes.data:Text"/>
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133 <datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/>
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134 <datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/>
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135 <datatype extension="pepstats" type="galaxy.datatypes.data:Text"/>
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136 <datatype extension="phylip" type="galaxy.datatypes.data:Text"/>
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137 <datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/>
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138 <datatype extension="pir" type="galaxy.datatypes.data:Text"/>
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139 <datatype extension="polydot" type="galaxy.datatypes.data:Text"/>
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140 <datatype extension="preg" type="galaxy.datatypes.data:Text"/>
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141 <datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/>
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142 <datatype extension="primersearch" type="galaxy.datatypes.data:Text"/>
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143 <datatype extension="regions" type="galaxy.datatypes.data:Text"/>
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144 <datatype extension="score" type="galaxy.datatypes.data:Text"/>
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145 <datatype extension="selex" type="galaxy.datatypes.data:Text"/>
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146 <datatype extension="seqtable" type="galaxy.datatypes.data:Text"/>
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147 <datatype extension="showfeat" type="galaxy.datatypes.data:Text"/>
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148 <datatype extension="showorf" type="galaxy.datatypes.data:Text"/>
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149 <datatype extension="simple" type="galaxy.datatypes.data:Text"/>
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150 <datatype extension="sixpack" type="galaxy.datatypes.data:Text"/>
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151 <datatype extension="srs" type="galaxy.datatypes.data:Text"/>
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152 <datatype extension="srspair" type="galaxy.datatypes.data:Text"/>
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153 <datatype extension="staden" type="galaxy.datatypes.data:Text"/>
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154 <datatype extension="strider" type="galaxy.datatypes.data:Text"/>
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155 <datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/>
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156 <datatype extension="swiss" type="galaxy.datatypes.data:Text"/>
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157 <datatype extension="syco" type="galaxy.datatypes.data:Text"/>
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158 <datatype extension="table" type="galaxy.datatypes.data:Text"/>
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159 <datatype extension="textsearch" type="galaxy.datatypes.data:Text"/>
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160 <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/>
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161 <datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
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162 <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
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163 <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
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164 <!-- End EMBOSS tools -->
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parents:
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165 <!-- Start ONTO-PERL tools -->
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166 <datatype extension="obo" type="galaxy.datatypes.data:Text"/>
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167 <!-- End ONTO-PERL tools -->
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parents:
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168 <!-- Start RGenetics Datatypes -->
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169 <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
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170 <!-- eigenstrat pedigree input file -->
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171 <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
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172 <!-- eigenstrat pca output file for adjusted eigenQTL eg -->
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173 <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
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174 <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" />
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175 <!-- fbat/pbat format pedigree (header row of marker names) -->
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176 <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
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177 <!-- phenotype file - fbat format -->
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178 <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
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179 <!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
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180 <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
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parents:
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181 <!-- part of linkage format pedigree -->
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182 <datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap" display_in_upload="true"/>
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183 <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
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184 <!-- linkage format pedigree (separate .map file) -->
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185 <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
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186 <converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
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187 <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
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188 </datatype>
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189 <!-- plink compressed file - has bed extension unfortunately -->
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parents:
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190 <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
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191 <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
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192 </datatype>
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193 <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
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194 <!-- phenotype file - plink format -->
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parents:
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195 <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/>
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196 <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
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parents:
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197 <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
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parents:
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198 <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
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199 <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
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200 <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
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201 <!-- End RGenetics Datatypes -->
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202 </registration>
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203 <sniffers>
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parents:
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204 <!--
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205 The order in which Galaxy attempts to determine data types is
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206 important because some formats are much more loosely defined
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parents:
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207 than others. The following list should be the most rigidly
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208 defined format first, followed by next-most rigidly defined,
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parents:
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209 and so on.
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easr
parents:
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210 -->
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easr
parents:
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211 <sniffer type="galaxy.datatypes.binary:Bam"/>
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easr
parents:
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212 <sniffer type="galaxy.datatypes.binary:Sff"/>
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easr
parents:
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213 <sniffer type="galaxy.datatypes.xml:BlastXml"/>
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easr
parents:
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214 <sniffer type="galaxy.datatypes.sequence:Maf"/>
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easr
parents:
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215 <sniffer type="galaxy.datatypes.sequence:Lav"/>
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easr
parents:
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216 <sniffer type="galaxy.datatypes.sequence:csFasta"/>
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easr
parents:
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217 <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
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easr
parents:
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218 <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
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easr
parents:
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219 <sniffer type="galaxy.datatypes.sequence:Fasta"/>
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easr
parents:
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220 <sniffer type="galaxy.datatypes.sequence:Fastq"/>
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easr
parents:
diff changeset
221 <sniffer type="galaxy.datatypes.interval:Wiggle"/>
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easr
parents:
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222 <sniffer type="galaxy.datatypes.images:Html"/>
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easr
parents:
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223 <sniffer type="galaxy.datatypes.sequence:Axt"/>
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easr
parents:
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224 <sniffer type="galaxy.datatypes.interval:Bed"/>
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easr
parents:
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225 <sniffer type="galaxy.datatypes.interval:CustomTrack"/>
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easr
parents:
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226 <sniffer type="galaxy.datatypes.interval:Gff"/>
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easr
parents:
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227 <sniffer type="galaxy.datatypes.interval:Gff3"/>
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easr
parents:
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228 <sniffer type="galaxy.datatypes.interval:Interval"/>
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easr
parents:
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229 <sniffer type="galaxy.datatypes.tabular:Sam"/>
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parents:
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230 </sniffers>
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231 </datatypes>