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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 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 </requirements>
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6 <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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7 <inputs>
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8 <param format="interval" name="input1" type="data" label="Choose Intervals">
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9 <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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10 </param>
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11 <param name="keep_empty" type="select" label="Keep Region/Table Pairs with 0 Coverage">
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12 <option value="-k">Keep</option>
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13 <option value="" selected="true">Discard</option>
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14 </param>
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15 <param name="summary" type="select" label="Output per Region/Summary">
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16 <option value="-S">Summary</option>
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17 <option value="" selected="true">Per Region</option>
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18 </param>
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19 <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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20 </inputs>
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21 <outputs>
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22 <data format="input" name="out_file1">
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23 <change_format>
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24 <when input="summary" value="-S" format="tabular" />
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25 </change_format>
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26 </data>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input1" value="4.bed" dbkey="hg18"/>
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31 <param name="keep_empty" value=""/>
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32 <param name="summary" value=""/>
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33 <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/>
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34 <output name="out_file1" file="annotation_profiler_1.out" />
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35 </test>
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36 <test>
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37 <param name="input1" value="3.bed" dbkey="hg18"/>
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38 <param name="keep_empty" value=""/>
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39 <param name="summary" value="Summary"/>
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40 <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/>
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41 <output name="out_file1" file="annotation_profiler_2.out" />
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42 </test>
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43 </tests>
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44 <help>
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45 **What it does**
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46
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47 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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48
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49 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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50
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51 You may alternatively choose to receive a summary across all of the intervals that you provide.
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52
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53 -----
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54
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55 **Example**
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56
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57 Using the interval below and selecting several tables::
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58
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59 chr1 4558 14764 uc001aab.1 0 -
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60
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61 results in::
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62
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63 chr1 4558 14764 uc001aab.1 0 - snp126Exceptions 151 142
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64 chr1 4558 14764 uc001aab.1 0 - genomicSuperDups 10206 1
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65 chr1 4558 14764 uc001aab.1 0 - chainOryLat1 3718 1
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66 chr1 4558 14764 uc001aab.1 0 - multiz28way 10206 1
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67 chr1 4558 14764 uc001aab.1 0 - affyHuEx1 3553 32
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68 chr1 4558 14764 uc001aab.1 0 - netXenTro2 3050 1
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69 chr1 4558 14764 uc001aab.1 0 - intronEst 10206 1
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70 chr1 4558 14764 uc001aab.1 0 - xenoMrna 10203 1
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71 chr1 4558 14764 uc001aab.1 0 - ctgPos 10206 1
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72 chr1 4558 14764 uc001aab.1 0 - clonePos 10206 1
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73 chr1 4558 14764 uc001aab.1 0 - chainStrPur2Link 1323 29
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74 chr1 4558 14764 uc001aab.1 0 - affyTxnPhase3HeLaNuclear 9011 8
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75 chr1 4558 14764 uc001aab.1 0 - snp126orthoPanTro2RheMac2 61 58
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76 chr1 4558 14764 uc001aab.1 0 - snp126 205 192
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77 chr1 4558 14764 uc001aab.1 0 - chainEquCab1 10206 1
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78 chr1 4558 14764 uc001aab.1 0 - netGalGal3 3686 1
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79 chr1 4558 14764 uc001aab.1 0 - phastCons28wayPlacMammal 10172 3
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80
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81 Where::
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82
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83 The first added column is the table name.
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84 The second added column is the number of bases covered by the table.
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85 The third added column is the number of regions from the table that is covered by the interval.
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86
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87 Alternatively, requesting a summary, using the intervals below and selecting several tables::
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88
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89 chr1 4558 14764 uc001aab.1 0 -
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90 chr1 4558 19346 uc001aac.1 0 -
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91
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92 results in::
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93
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94 #tableName tableSize tableRegionCount allIntervalCount allIntervalSize allCoverage allTableRegionsOverlaped allIntervalsOverlapingTable nrIntervalCount nrIntervalSize nrCoverage nrTableRegionsOverlaped nrIntervalsOverlapingTable
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95 snp126Exceptions 133601 92469 2 24994 388 359 2 1 14788 237 217 1
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96 genomicSuperDups 12268847 657 2 24994 24994 2 2 1 14788 14788 1 1
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97 chainOryLat1 70337730 2542 2 24994 7436 2 2 1 14788 3718 1 1
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98 affyHuEx1 15703901 112274 2 24994 7846 70 2 1 14788 4293 38 1
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99 netXenTro2 111440392 1877 2 24994 6100 2 2 1 14788 3050 1 1
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100 snp126orthoPanTro2RheMac2 700436 690674 2 24994 124 118 2 1 14788 63 60 1
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101 intronEst 135796064 2332 2 24994 24994 2 2 1 14788 14788 1 1
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102 xenoMrna 129031327 1586 2 24994 20406 2 2 1 14788 10203 1 1
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103 snp126 956976 838091 2 24994 498 461 2 1 14788 293 269 1
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104 clonePos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1
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105 chainStrPur2Link 7948016 119841 2 24994 2646 58 2 1 14788 1323 29 1
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106 affyTxnPhase3HeLaNuclear 136797870 140244 2 24994 22601 17 2 1 14788 13590 9 1
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107 multiz28way 225928588 38 2 24994 24994 2 2 1 14788 14788 1 1
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108 ctgPos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1
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109 chainEquCab1 246306414 141 2 24994 24994 2 2 1 14788 14788 1 1
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110 netGalGal3 203351973 461 2 24994 7372 2 2 1 14788 3686 1 1
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111 phastCons28wayPlacMammal 221017670 22803 2 24994 24926 6 2 1 14788 14754 3 1
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112
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113 Where::
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114
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115 tableName is the name of the table
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116 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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117 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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118 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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119 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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120
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121 allIntervalCount is the number of provided intervals
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122 allIntervalSize is the sum of the lengths of the provided interval file
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123 allCoverage is the sum of the coverage for each provided interval
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124 allTableRegionsOverlapped is the sum of the number of regions of the table (non-unique) that were overlapped for each interval
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125 allIntervalsOverlappingTable is the number of provided intervals which overlap the table
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126
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127 nrIntervalCount is the number of non-redundant intervals
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128 nrIntervalSize is the sum of the lengths of non-redundant intervals
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129 nrCoverage is the sum of the coverage of non-redundant intervals
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130 nrTableRegionsOverlapped is the number of regions of the table (unique) that were overlapped by the non-redundant intervals
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131 nrIntervalsOverlappingTable is the number of non-redundant intervals which overlap the table
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132
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133
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134 .. class:: infomark
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135
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136 **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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137
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138 ------
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139
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140 **Citation**
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141
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142 For the underlying data, please see http://genome.ucsc.edu/cite.html for the proper citation.
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143
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144 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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145
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146 </help>
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147 </tool>
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