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1 <tool id="Annotation_Profiler_0" name="Profile Annotations" version="1.0.0">
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2 <description>for a set of genomic intervals</description>
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3 <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p ${GALAXY_DATA_INDEX_DIR}/annotation_profiler/$dbkey $summary -b 3 -t $table_names</command>
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4 <inputs>
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5 <param format="interval" name="input1" type="data" label="Choose Intervals">
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6 <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/>
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7 </param>
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8 <param name="keep_empty" type="select" label="Keep Region/Table Pairs with 0 Coverage">
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9 <option value="-k">Keep</option>
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10 <option value="" selected="true">Discard</option>
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11 </param>
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12 <param name="summary" type="select" label="Output per Region/Summary">
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13 <option value="-S">Summary</option>
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14 <option value="" selected="true">Per Region</option>
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15 </param>
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16 <param name="table_names" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Tables to Use" help="Selecting no tables will result in using all tables." from_file="annotation_profiler_options.xml"/>
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17 </inputs>
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18 <outputs>
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19 <data format="input" name="out_file1">
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20 <change_format>
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21 <when input="summary" value="-S" format="tabular" />
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22 </change_format>
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23 </data>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input1" value="4.bed" dbkey="hg18"/>
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28 <param name="keep_empty" value=""/>
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29 <param name="summary" value=""/>
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30 <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/>
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31 <output name="out_file1" file="annotation_profiler_1.out" />
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32 </test>
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33 <test>
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34 <param name="input1" value="3.bed" dbkey="hg18"/>
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35 <param name="keep_empty" value=""/>
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36 <param name="summary" value="Summary"/>
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37 <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/>
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38 <output name="out_file1" file="annotation_profiler_2.out" />
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39 </test>
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40 </tests>
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41 <help>
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42 **What it does**
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43
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44 Takes an input set of intervals and for each interval determines the base coverage of the interval by a set of features (tables) available from UCSC. Genomic regions from the input feature data have been merged by overlap / direct adjacency (e.g. a table having ranges of: 1-10, 6-12, 12-20 and 25-28 results in two merged ranges of: 1-20 and 25-28).
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45
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46 By default, this tool will check the coverage of your intervals against all available features; you may, however, choose to select only those tables that you want to include. Selecting a section heading will effectively cause all of its children to be selected.
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47
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48 You may alternatively choose to receive a summary across all of the intervals that you provide.
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49
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50 -----
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51
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52 **Example**
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53
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54 Using the interval below and selecting several tables::
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55
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56 chr1 4558 14764 uc001aab.1 0 -
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57
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58 results in::
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59
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60 chr1 4558 14764 uc001aab.1 0 - snp126Exceptions 151 142
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61 chr1 4558 14764 uc001aab.1 0 - genomicSuperDups 10206 1
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62 chr1 4558 14764 uc001aab.1 0 - chainOryLat1 3718 1
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63 chr1 4558 14764 uc001aab.1 0 - multiz28way 10206 1
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64 chr1 4558 14764 uc001aab.1 0 - affyHuEx1 3553 32
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65 chr1 4558 14764 uc001aab.1 0 - netXenTro2 3050 1
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66 chr1 4558 14764 uc001aab.1 0 - intronEst 10206 1
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67 chr1 4558 14764 uc001aab.1 0 - xenoMrna 10203 1
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68 chr1 4558 14764 uc001aab.1 0 - ctgPos 10206 1
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69 chr1 4558 14764 uc001aab.1 0 - clonePos 10206 1
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70 chr1 4558 14764 uc001aab.1 0 - chainStrPur2Link 1323 29
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71 chr1 4558 14764 uc001aab.1 0 - affyTxnPhase3HeLaNuclear 9011 8
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72 chr1 4558 14764 uc001aab.1 0 - snp126orthoPanTro2RheMac2 61 58
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73 chr1 4558 14764 uc001aab.1 0 - snp126 205 192
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74 chr1 4558 14764 uc001aab.1 0 - chainEquCab1 10206 1
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75 chr1 4558 14764 uc001aab.1 0 - netGalGal3 3686 1
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76 chr1 4558 14764 uc001aab.1 0 - phastCons28wayPlacMammal 10172 3
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77
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78 Where::
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79
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80 The first added column is the table name.
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81 The second added column is the number of bases covered by the table.
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82 The third added column is the number of regions from the table that is covered by the interval.
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83
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84 Alternatively, requesting a summary, using the intervals below and selecting several tables::
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85
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86 chr1 4558 14764 uc001aab.1 0 -
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87 chr1 4558 19346 uc001aac.1 0 -
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88
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89 results in::
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90
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91 #tableName tableSize tableRegionCount allIntervalCount allIntervalSize allCoverage allTableRegionsOverlaped allIntervalsOverlapingTable nrIntervalCount nrIntervalSize nrCoverage nrTableRegionsOverlaped nrIntervalsOverlapingTable
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92 snp126Exceptions 133601 92469 2 24994 388 359 2 1 14788 237 217 1
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93 genomicSuperDups 12268847 657 2 24994 24994 2 2 1 14788 14788 1 1
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94 chainOryLat1 70337730 2542 2 24994 7436 2 2 1 14788 3718 1 1
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95 affyHuEx1 15703901 112274 2 24994 7846 70 2 1 14788 4293 38 1
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96 netXenTro2 111440392 1877 2 24994 6100 2 2 1 14788 3050 1 1
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97 snp126orthoPanTro2RheMac2 700436 690674 2 24994 124 118 2 1 14788 63 60 1
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98 intronEst 135796064 2332 2 24994 24994 2 2 1 14788 14788 1 1
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99 xenoMrna 129031327 1586 2 24994 20406 2 2 1 14788 10203 1 1
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100 snp126 956976 838091 2 24994 498 461 2 1 14788 293 269 1
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101 clonePos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1
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102 chainStrPur2Link 7948016 119841 2 24994 2646 58 2 1 14788 1323 29 1
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103 affyTxnPhase3HeLaNuclear 136797870 140244 2 24994 22601 17 2 1 14788 13590 9 1
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104 multiz28way 225928588 38 2 24994 24994 2 2 1 14788 14788 1 1
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105 ctgPos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1
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106 chainEquCab1 246306414 141 2 24994 24994 2 2 1 14788 14788 1 1
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107 netGalGal3 203351973 461 2 24994 7372 2 2 1 14788 3686 1 1
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108 phastCons28wayPlacMammal 221017670 22803 2 24994 24926 6 2 1 14788 14754 3 1
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109
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110 Where::
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111
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112 tableName is the name of the table
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113 tableChromosomeCoverage is the number of positions existing in the table for only the chromosomes that were referenced by the interval file
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114 tableChromosomeCount is the number of regions existing in the table for only the chromosomes that were referenced by the interval file
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115 tableRegionCoverage is the number of positions existing in the table between the minimal and maximal bounding regions that were referenced by the interval file
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116 tableRegionCount is the number of regions existing in the table between the minimal and maximal bounding regions that were referenced by the interval file
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117
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118 allIntervalCount is the number of provided intervals
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119 allIntervalSize is the sum of the lengths of the provided interval file
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120 allCoverage is the sum of the coverage for each provided interval
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121 allTableRegionsOverlapped is the sum of the number of regions of the table (non-unique) that were overlapped for each interval
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122 allIntervalsOverlappingTable is the number of provided intervals which overlap the table
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123
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124 nrIntervalCount is the number of non-redundant intervals
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125 nrIntervalSize is the sum of the lengths of non-redundant intervals
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126 nrCoverage is the sum of the coverage of non-redundant intervals
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127 nrTableRegionsOverlapped is the number of regions of the table (unique) that were overlapped by the non-redundant intervals
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128 nrIntervalsOverlappingTable is the number of non-redundant intervals which overlap the table
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129
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130
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131 .. class:: infomark
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132
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133 **TIP:** non-redundant (nr) refers to the set of intervals that remains after the intervals provided have been merged to resolve overlaps
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134
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135 </help>
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136 </tool>
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