[2] | 1 | <tool id="rgHaploView1" name="LD plots:"> |
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| 2 | <code file="rgHaploView_code.py"/> |
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| 3 | |
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| 4 | <description>and comparisons with HapMap data</description> |
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| 5 | |
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| 6 | <command interpreter="python"> |
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| 7 | rgHaploView.py "$ucsc_region" "$rslist" "$title" "$out_file1" |
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| 8 | "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name" |
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| 9 | "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$out_file1.files_path" |
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| 10 | "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/shared/jars/haploview.jar |
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| 11 | </command> |
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| 12 | |
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| 13 | <inputs> |
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| 14 | |
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| 15 | <param name="lhistIn" type="data" format="lped" |
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| 16 | label="Current history lPed format data" |
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| 17 | size="80" help="Linkage Ped format data from your current history" /> |
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| 18 | |
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| 19 | <param name="ucsc_region" type="text" label="Optional subset region (blank=ALL)" |
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| 20 | size="80" optional="true" |
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| 21 | help="Region eg: chr9:119,506,000-119,518,000 Leave blank for all or to extract the rs list supplied below."/> |
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| 22 | |
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| 23 | <param name="rslist" type="text" area='true' size='5x20' label="rs list" optional="true" |
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| 24 | help="List of rs numbers to select - cut and paste or type, use space delimiters. Leave blank to extract region supplied above." /> |
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| 25 | |
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| 26 | <param name="title" type="text" size="80" label="Title for output files" optional="true" |
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| 27 | help="Descriptive title for new genotype/map files" value="LD Plots" /> |
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| 28 | |
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| 29 | <param name="ldtype" type="select" label="Type of LD measure to estimate and plot" |
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| 30 | size="80" help="" > |
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| 31 | <option value="RSQ" selected="True">rsquared (default)</option> |
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| 32 | <option value="DEFAULT">D prime</option> |
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| 33 | <option value="DPALT">D prime alternative</option> |
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| 34 | <option value="GAB">Gabriel</option> |
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| 35 | <option value="GAM">4 Gamete test</option> |
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| 36 | </param> |
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| 37 | |
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| 38 | <param name="minmaf" type="float" label = "Minimum minor allele frequency to use" value="0.05" |
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| 39 | help="If > 0.0, markers below this MAF will be ignored for calculations"/> |
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| 40 | |
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| 41 | <param name="maxdist" type="integer" label = "Maximum distance (kbp) between markers for LD estimate" |
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| 42 | value="200" help="If < > 0, only marker pairs at or below this distance will have LD calculated"/> |
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| 43 | |
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| 44 | <param name="hmpanel" type="select" multiple="true" label="Hapmap panels to compare" |
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| 45 | size="40" help="HapMap data LD plots will also be produced for each selected population panel" > |
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| 46 | <option value='CEU' selected="True">CEPH (European) (default)</option> |
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| 47 | <option value='YRI'>Yoruba (African)</option> |
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| 48 | <option value='CHB+JPT'>Chinese + Japanese</option> |
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| 49 | <option value="">(None - no comparison)</option> |
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| 50 | </param> |
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| 51 | <param name="tagr2" type="float" label = "rsquared threshold for tagging outputs" value="0.8" |
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| 52 | help="Tagging output will use this value as the minimum rsquared threshold"/> |
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| 53 | |
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| 54 | <param name="infoTrack" type="select" label="Add Hapmap information track to image" |
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| 55 | help="Refseq genes and snp density can be added to the plot if desired for orientation" > |
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| 56 | <option value="info">Add Information track (DISABLED! Awaiting fix from Haploview authors)</option> |
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| 57 | <option value="noinfo" selected="True">No Information track</option> |
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| 58 | </param> |
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| 59 | |
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| 60 | <param name="hires" type="select" label="High resolution plots" |
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| 61 | help="A high resolution plot file may be possible but only for small regions - not reliable >100's of snps"> |
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| 62 | <option value="hi">High resolution - only a few (hundreds of) markers</option> |
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| 63 | <option value="lo" selected="True">Low resolution - large number of markers</option> |
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| 64 | </param> |
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| 65 | |
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| 66 | <param name="memsize" type="select" label="System RAM to allocate" |
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| 67 | size="80" help="Very large files will need extra memory (java is a bit of a pig)" > |
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| 68 | <option value="1024">1GB</option> |
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| 69 | <option value="2048" selected="True">2GB (default)</option> |
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| 70 | <option value="4096">4GB</option> |
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| 71 | <option value="6144">6GB</option> |
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| 72 | <option value="8192">8GB</option> |
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| 73 | </param> |
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| 74 | |
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| 75 | </inputs> |
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| 76 | |
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| 77 | <outputs> |
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| 78 | <data format="html" name="out_file1" /> |
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| 79 | |
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| 80 | </outputs> |
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| 81 | |
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| 82 | <!-- python $TOOLPATH/$TOOL.py "" "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \ |
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| 83 | "$NPRE" $OUTPATH/${NPRE}.html "test" "" "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "hg18" "noinfo" "0.8" \ |
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| 84 | "['CEU','YRI','CHB+JPT']" $BINPATH/haploview.jar --> |
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| 85 | <tests> |
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| 86 | <test> |
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| 87 | <param name='lhistIn' value='tinywga' ftype='lped' > |
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| 88 | <metadata name='base_name' value='tinywga' /> |
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| 89 | <composite_data value='tinywga.ped' /> |
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| 90 | <composite_data value='tinywga.map' /> |
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| 91 | <edit_attributes type='name' value='tinywga' /> |
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| 92 | </param> |
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| 93 | <param name='ucsc_region' value='' /> |
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| 94 | <param name='title' value='rgHaploViewtest1' /> |
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| 95 | <param name='rslist' value="rs2283802 rs2267000 rs16997606 rs4820537 rs3788347 rs756632Xrs4820539 rs2283804 rs2267006 rs4822363" /> |
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| 96 | <param name='ldtype' value='RSQ' /> |
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| 97 | <param name='minmaf' value='0.0' /> |
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| 98 | <param name='maxdist' value='200000' /> |
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| 99 | <param name='tagr2' value='0.8' /> |
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| 100 | <param name='hmpanel' value="YRI" /> |
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| 101 | <param name='infoTrack' value='noinfo' /> |
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| 102 | <param name='hires' value='lo' /> |
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| 103 | <param name='memsize' value='2048' /> |
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| 104 | <output name='out_file1' file='rgtestouts/rgHaploView/rgHaploViewtest1.html' ftype='html' lines_diff="50"> |
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| 105 | <extra_files type="file" name='alljoin.pdf' value="rgtestouts/rgHaploView/alljoin.pdf" compare="sim_size" delta="3000"/> |
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| 106 | <extra_files type="file" name='allnup.pdf' value="rgtestouts/rgHaploView/allnup.pdf" compare="sim_size" delta="3000" /> |
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| 107 | <extra_files type="file" name='Log_rgHaploViewtest1.txt' value="rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt" compare="diff" lines_diff="50"/> |
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| 108 | <extra_files type="file" name='rgHaploViewtest1.ped.TESTS' value="rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS" compare="diff" |
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| 109 | lines_diff="20"/> |
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| 110 | <extra_files type="file" name='rgHaploViewtest1.ped.TAGS' value="rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS" compare="diff" |
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| 111 | lines_diff="20" /> |
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| 112 | </output> |
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| 113 | </test> |
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| 114 | </tests> |
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| 115 | |
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| 116 | <help> |
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| 117 | |
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| 118 | .. class:: infomark |
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| 119 | |
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| 120 | **Note** |
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| 121 | |
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| 122 | The input file must be in linkage ped format. A suitable file can be chosen from the system library, |
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| 123 | or from the files already imported into your current history. Use either one of the selection boxes to |
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| 124 | make your choice. |
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| 125 | |
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| 126 | ----- |
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| 127 | |
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| 128 | **Syntax** |
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| 129 | |
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| 130 | - **Library Linkage Ped** is a linkage format pedigree file chosen from the system file Library |
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| 131 | - **History Linkage Ped** is a linkage format pedigree file chosen from your current Galaxy History |
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| 132 | - **Region** is the genomic region cut and paste from a UCSC browser location window |
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| 133 | - **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data |
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| 134 | |
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| 135 | ----- |
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| 136 | |
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| 137 | **Summary** |
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| 138 | |
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| 139 | This tool is a special purpose tool to estimate and plot linkage disequilibrium estimated |
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| 140 | from genotype data in linkage pedigree format (separate map file). All markers in the input file |
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| 141 | are used as the default. To limit the calculations to a subset of the input data, supply |
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| 142 | a specified genomic region in UCSC browser location format or a list of specific marker IDs. |
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| 143 | |
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| 144 | Note that you can choose either a file of the correct type (linkage pedigree - lped) from |
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| 145 | your current history **or** from the system library |
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| 146 | |
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| 147 | This tool currently calls Haploview for estimation and plots. For full attribution, source code and documentation, see |
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| 148 | http://www.broad.mit.edu/mpg/haploview/index.php |
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| 149 | |
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| 150 | Copyright, Ross Lazarus, April 2008 for the Rgenetics project |
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| 151 | Released under the LGPL. See http://www.gnu.org/licenses/lgpl.html for license terms. |
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| 152 | |
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| 153 | </help> |
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| 154 | </tool> |
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