Mercurial > repos > xuebing > sharplabtool
comparison tools/annotation_profiler/annotation_profiler.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="Annotation_Profiler_0" name="Profile Annotations" version="1.0.0"> | |
2 <description>for a set of genomic intervals</description> | |
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> | |
4 <inputs> | |
5 <param format="interval" name="input1" type="data" label="Choose Intervals"> | |
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."/> | |
7 </param> | |
8 <param name="keep_empty" type="select" label="Keep Region/Table Pairs with 0 Coverage"> | |
9 <option value="-k">Keep</option> | |
10 <option value="" selected="true">Discard</option> | |
11 </param> | |
12 <param name="summary" type="select" label="Output per Region/Summary"> | |
13 <option value="-S">Summary</option> | |
14 <option value="" selected="true">Per Region</option> | |
15 </param> | |
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"/> | |
17 </inputs> | |
18 <outputs> | |
19 <data format="input" name="out_file1"> | |
20 <change_format> | |
21 <when input="summary" value="-S" format="tabular" /> | |
22 </change_format> | |
23 </data> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="input1" value="4.bed" dbkey="hg18"/> | |
28 <param name="keep_empty" value=""/> | |
29 <param name="summary" value=""/> | |
30 <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/> | |
31 <output name="out_file1" file="annotation_profiler_1.out" /> | |
32 </test> | |
33 <test> | |
34 <param name="input1" value="3.bed" dbkey="hg18"/> | |
35 <param name="keep_empty" value=""/> | |
36 <param name="summary" value="Summary"/> | |
37 <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/> | |
38 <output name="out_file1" file="annotation_profiler_2.out" /> | |
39 </test> | |
40 </tests> | |
41 <help> | |
42 **What it does** | |
43 | |
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). | |
45 | |
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. | |
47 | |
48 You may alternatively choose to receive a summary across all of the intervals that you provide. | |
49 | |
50 ----- | |
51 | |
52 **Example** | |
53 | |
54 Using the interval below and selecting several tables:: | |
55 | |
56 chr1 4558 14764 uc001aab.1 0 - | |
57 | |
58 results in:: | |
59 | |
60 chr1 4558 14764 uc001aab.1 0 - snp126Exceptions 151 142 | |
61 chr1 4558 14764 uc001aab.1 0 - genomicSuperDups 10206 1 | |
62 chr1 4558 14764 uc001aab.1 0 - chainOryLat1 3718 1 | |
63 chr1 4558 14764 uc001aab.1 0 - multiz28way 10206 1 | |
64 chr1 4558 14764 uc001aab.1 0 - affyHuEx1 3553 32 | |
65 chr1 4558 14764 uc001aab.1 0 - netXenTro2 3050 1 | |
66 chr1 4558 14764 uc001aab.1 0 - intronEst 10206 1 | |
67 chr1 4558 14764 uc001aab.1 0 - xenoMrna 10203 1 | |
68 chr1 4558 14764 uc001aab.1 0 - ctgPos 10206 1 | |
69 chr1 4558 14764 uc001aab.1 0 - clonePos 10206 1 | |
70 chr1 4558 14764 uc001aab.1 0 - chainStrPur2Link 1323 29 | |
71 chr1 4558 14764 uc001aab.1 0 - affyTxnPhase3HeLaNuclear 9011 8 | |
72 chr1 4558 14764 uc001aab.1 0 - snp126orthoPanTro2RheMac2 61 58 | |
73 chr1 4558 14764 uc001aab.1 0 - snp126 205 192 | |
74 chr1 4558 14764 uc001aab.1 0 - chainEquCab1 10206 1 | |
75 chr1 4558 14764 uc001aab.1 0 - netGalGal3 3686 1 | |
76 chr1 4558 14764 uc001aab.1 0 - phastCons28wayPlacMammal 10172 3 | |
77 | |
78 Where:: | |
79 | |
80 The first added column is the table name. | |
81 The second added column is the number of bases covered by the table. | |
82 The third added column is the number of regions from the table that is covered by the interval. | |
83 | |
84 Alternatively, requesting a summary, using the intervals below and selecting several tables:: | |
85 | |
86 chr1 4558 14764 uc001aab.1 0 - | |
87 chr1 4558 19346 uc001aac.1 0 - | |
88 | |
89 results in:: | |
90 | |
91 #tableName tableSize tableRegionCount allIntervalCount allIntervalSize allCoverage allTableRegionsOverlaped allIntervalsOverlapingTable nrIntervalCount nrIntervalSize nrCoverage nrTableRegionsOverlaped nrIntervalsOverlapingTable | |
92 snp126Exceptions 133601 92469 2 24994 388 359 2 1 14788 237 217 1 | |
93 genomicSuperDups 12268847 657 2 24994 24994 2 2 1 14788 14788 1 1 | |
94 chainOryLat1 70337730 2542 2 24994 7436 2 2 1 14788 3718 1 1 | |
95 affyHuEx1 15703901 112274 2 24994 7846 70 2 1 14788 4293 38 1 | |
96 netXenTro2 111440392 1877 2 24994 6100 2 2 1 14788 3050 1 1 | |
97 snp126orthoPanTro2RheMac2 700436 690674 2 24994 124 118 2 1 14788 63 60 1 | |
98 intronEst 135796064 2332 2 24994 24994 2 2 1 14788 14788 1 1 | |
99 xenoMrna 129031327 1586 2 24994 20406 2 2 1 14788 10203 1 1 | |
100 snp126 956976 838091 2 24994 498 461 2 1 14788 293 269 1 | |
101 clonePos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1 | |
102 chainStrPur2Link 7948016 119841 2 24994 2646 58 2 1 14788 1323 29 1 | |
103 affyTxnPhase3HeLaNuclear 136797870 140244 2 24994 22601 17 2 1 14788 13590 9 1 | |
104 multiz28way 225928588 38 2 24994 24994 2 2 1 14788 14788 1 1 | |
105 ctgPos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1 | |
106 chainEquCab1 246306414 141 2 24994 24994 2 2 1 14788 14788 1 1 | |
107 netGalGal3 203351973 461 2 24994 7372 2 2 1 14788 3686 1 1 | |
108 phastCons28wayPlacMammal 221017670 22803 2 24994 24926 6 2 1 14788 14754 3 1 | |
109 | |
110 Where:: | |
111 | |
112 tableName is the name of the table | |
113 tableChromosomeCoverage is the number of positions existing in the table for only the chromosomes that were referenced by the interval file | |
114 tableChromosomeCount is the number of regions existing in the table for only the chromosomes that were referenced by the interval file | |
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 | |
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 | |
117 | |
118 allIntervalCount is the number of provided intervals | |
119 allIntervalSize is the sum of the lengths of the provided interval file | |
120 allCoverage is the sum of the coverage for each provided interval | |
121 allTableRegionsOverlapped is the sum of the number of regions of the table (non-unique) that were overlapped for each interval | |
122 allIntervalsOverlappingTable is the number of provided intervals which overlap the table | |
123 | |
124 nrIntervalCount is the number of non-redundant intervals | |
125 nrIntervalSize is the sum of the lengths of non-redundant intervals | |
126 nrCoverage is the sum of the coverage of non-redundant intervals | |
127 nrTableRegionsOverlapped is the number of regions of the table (unique) that were overlapped by the non-redundant intervals | |
128 nrIntervalsOverlappingTable is the number of non-redundant intervals which overlap the table | |
129 | |
130 | |
131 .. class:: infomark | |
132 | |
133 **TIP:** non-redundant (nr) refers to the set of intervals that remains after the intervals provided have been merged to resolve overlaps | |
134 | |
135 </help> | |
136 </tool> |