mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
137 lines
7.3 KiB
XML
137 lines
7.3 KiB
XML
<tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0">
|
|
<description>for a set of genomic intervals</description>
|
|
<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 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${chromInfo} -b 3 -t $table_names</command>
|
|
<inputs>
|
|
<param format="interval" name="input1" type="data" label="Choose Intervals">
|
|
<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."/>
|
|
</param>
|
|
<param name="keep_empty" type="select" label="Keep Region/Table Pairs with 0 Coverage">
|
|
<option value="-k">Keep</option>
|
|
<option value="" selected="true">Discard</option>
|
|
</param>
|
|
<param name="summary" type="select" label="Output per Region/Summary">
|
|
<option value="-S">Summary</option>
|
|
<option value="" selected="true">Per Region</option>
|
|
</param>
|
|
<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"/>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="input" name="out_file1">
|
|
<change_format>
|
|
<when input="summary" value="-S" format="tabular" />
|
|
</change_format>
|
|
</data>
|
|
</outputs>
|
|
<tests>
|
|
<test>
|
|
<param name="input1" value="4.bed" dbkey="hg18"/>
|
|
<param name="keep_empty" value=""/>
|
|
<param name="summary" value=""/>
|
|
<param name="table_names" value="acembly,affyGnf1h,affyHuEx1,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/>
|
|
<output name="out_file1" file="annotation_profiler_1.out" />
|
|
</test>
|
|
<test>
|
|
<param name="input1" value="3.bed" dbkey="hg18"/>
|
|
<param name="keep_empty" value=""/>
|
|
<param name="summary" value="Summary"/>
|
|
<param name="table_names" value="acembly,affyGnf1h,affyHuEx1,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/>
|
|
<output name="out_file1" file="annotation_profiler_2.out" />
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
**What it does**
|
|
|
|
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.
|
|
|
|
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.
|
|
|
|
You may alternatively choose to receive a summary across all of the intervals that you provide.
|
|
|
|
-----
|
|
|
|
**Example**
|
|
|
|
Using the interval below and selecting several tables::
|
|
|
|
chr1 4558 14764 uc001aab.1 0 -
|
|
|
|
results in::
|
|
|
|
chr1 4558 14764 uc001aab.1 0 - snp126Exceptions 151 142
|
|
chr1 4558 14764 uc001aab.1 0 - genomicSuperDups 10206 1
|
|
chr1 4558 14764 uc001aab.1 0 - chainOryLat1 3718 1
|
|
chr1 4558 14764 uc001aab.1 0 - multiz28way 10206 1
|
|
chr1 4558 14764 uc001aab.1 0 - affyHuEx1 3553 32
|
|
chr1 4558 14764 uc001aab.1 0 - netXenTro2 3050 1
|
|
chr1 4558 14764 uc001aab.1 0 - intronEst 10206 1
|
|
chr1 4558 14764 uc001aab.1 0 - xenoMrna 10203 1
|
|
chr1 4558 14764 uc001aab.1 0 - ctgPos 10206 1
|
|
chr1 4558 14764 uc001aab.1 0 - clonePos 10206 1
|
|
chr1 4558 14764 uc001aab.1 0 - chainStrPur2Link 1323 29
|
|
chr1 4558 14764 uc001aab.1 0 - affyTxnPhase3HeLaNuclear 9011 8
|
|
chr1 4558 14764 uc001aab.1 0 - snp126orthoPanTro2RheMac2 61 58
|
|
chr1 4558 14764 uc001aab.1 0 - snp126 205 192
|
|
chr1 4558 14764 uc001aab.1 0 - chainEquCab1 10206 1
|
|
chr1 4558 14764 uc001aab.1 0 - netGalGal3 3686 1
|
|
chr1 4558 14764 uc001aab.1 0 - phastCons28wayPlacMammal 10172 3
|
|
|
|
Where::
|
|
|
|
The first added column is the table name.
|
|
The second added column is the number of bases covered by the table.
|
|
The third added column is the number of regions from the table that is covered by the interval.
|
|
|
|
Alternatively, requesting a summary, using the intervals below and selecting several tables::
|
|
|
|
chr1 4558 14764 uc001aab.1 0 -
|
|
chr1 4558 19346 uc001aac.1 0 -
|
|
|
|
results in::
|
|
|
|
#tableName tableSize tableRegionCount allIntervalCount allIntervalSize allCoverage allTableRegionsOverlaped allIntervalsOverlapingTable nrIntervalCount nrIntervalSize nrCoverage nrTableRegionsOverlaped nrIntervalsOverlapingTable
|
|
snp126Exceptions 133601 92469 2 24994 388 359 2 1 14788 237 217 1
|
|
genomicSuperDups 12268847 657 2 24994 24994 2 2 1 14788 14788 1 1
|
|
chainOryLat1 70337730 2542 2 24994 7436 2 2 1 14788 3718 1 1
|
|
affyHuEx1 15703901 112274 2 24994 7846 70 2 1 14788 4293 38 1
|
|
netXenTro2 111440392 1877 2 24994 6100 2 2 1 14788 3050 1 1
|
|
snp126orthoPanTro2RheMac2 700436 690674 2 24994 124 118 2 1 14788 63 60 1
|
|
intronEst 135796064 2332 2 24994 24994 2 2 1 14788 14788 1 1
|
|
xenoMrna 129031327 1586 2 24994 20406 2 2 1 14788 10203 1 1
|
|
snp126 956976 838091 2 24994 498 461 2 1 14788 293 269 1
|
|
clonePos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1
|
|
chainStrPur2Link 7948016 119841 2 24994 2646 58 2 1 14788 1323 29 1
|
|
affyTxnPhase3HeLaNuclear 136797870 140244 2 24994 22601 17 2 1 14788 13590 9 1
|
|
multiz28way 225928588 38 2 24994 24994 2 2 1 14788 14788 1 1
|
|
ctgPos 224999719 39 2 24994 24994 2 2 1 14788 14788 1 1
|
|
chainEquCab1 246306414 141 2 24994 24994 2 2 1 14788 14788 1 1
|
|
netGalGal3 203351973 461 2 24994 7372 2 2 1 14788 3686 1 1
|
|
phastCons28wayPlacMammal 221017670 22803 2 24994 24926 6 2 1 14788 14754 3 1
|
|
|
|
Where::
|
|
|
|
tableName is the name of the table
|
|
tableChromosomeCoverage is the number of positions existing in the table for only the chromosomes that were referenced by the interval file
|
|
tableChromosomeCount is the number of regions existing in the table for only the chromosomes that were referenced by the interval file
|
|
tableRegionCoverage is the number of positions existing in the table between the minimal and maximal bounding regions that were referenced by the interval file
|
|
tableRegionCount is the number of regions existing in the table between the minimal and maximal bounding regions that were referenced by the interval file
|
|
|
|
allIntervalCount is the number of provided intervals
|
|
allIntervalSize is the sum of the lengths of the provided interval file
|
|
allCoverage is the sum of the coverage for each provided interval
|
|
allTableRegionsOverlapped is the sum of the number of regions of the table (non-unique) that were overlapped for each interval
|
|
allIntervalsOverlappingTable is the number of provided intervals which overlap the table
|
|
|
|
nrIntervalCount is the number of non-redundant intervals
|
|
nrIntervalSize is the sum of the lengths of non-redundant intervals
|
|
nrCoverage is the sum of the coverage of non-redundant intervals
|
|
nrTableRegionsOverlapped is the number of regions of the table (unique) that were overlapped by the non-redundant intervals
|
|
nrIntervalsOverlappingTable is the number of non-redundant intervals which overlap the table
|
|
|
|
|
|
.. class:: infomark
|
|
|
|
**TIP:** non-redundant (nr) refers to the set of intervals that remains after the intervals provided have been merged to resolve overlaps
|
|
|
|
</help>
|
|
</tool>
|