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1 <tool id="rgHaploView1" name="LD plots:" version="0.3">
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2
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3 <description>and comparisons with HapMap data</description>
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4
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5 <command interpreter="python">
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6 rgHaploView.py "$ucsc_region" "$rslist" "$title" "$out_file1"
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7 "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name"
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8 "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$out_file1.files_path"
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9 "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/shared/jars/haploview.jar
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10 </command>
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11
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12 <inputs>
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13
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14 <param name="lhistIn" type="data" format="lped"
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15 label="Current history lPed format data"
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16 size="80" help="Linkage Ped format data from your current history" />
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17
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18 <param name="ucsc_region" type="text" label="Optional subset region (blank=ALL. WARNING: doing this will fail if >1 chromosome in input data!)"
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19 size="80" optional="true"
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20 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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21
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22 <param name="rslist" type="text" area='true' size='5x20' label="rs list" optional="true"
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23 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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24
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25 <param name="title" type="text" size="80" label="Title for output files" optional="true"
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26 help="Descriptive title for new genotype/map files" value="LD Plots" />
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27
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28 <param name="ldtype" type="select" label="Type of LD measure to estimate and plot"
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29 size="80" help="" >
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30 <option value="RSQ" selected="True">rsquared (default)</option>
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31 <option value="DEFAULT">D prime</option>
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32 <option value="DPALT">D prime alternative</option>
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33 <option value="GAB">Gabriel</option>
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34 <option value="GAM">4 Gamete test</option>
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35 </param>
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36
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37 <param name="minmaf" type="float" label = "Minimum minor allele frequency to use" value="0.05"
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38 help="If > 0.0, markers below this MAF will be ignored for calculations"/>
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39
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40 <param name="maxdist" type="integer" label = "Maximum distance (kbp) between markers for LD estimate"
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41 value="200" help="If < > 0, only marker pairs at or below this distance will have LD calculated"/>
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42
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43 <param name="hmpanel" type="select" multiple="true" label="Hapmap panels to compare"
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44 size="40" help="HapMap data LD plots will also be produced for each selected population panel" >
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45 <option value='CEU' selected="True">CEPH (European) (default)</option>
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46 <option value='YRI'>Yoruba (African)</option>
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47 <option value='CHB+JPT'>Chinese + Japanese</option>
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48 <option value="">(None - no comparison)</option>
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49 </param>
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50 <param name="tagr2" type="float" label = "rsquared threshold for tagging outputs" value="0.8"
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51 help="Tagging output will use this value as the minimum rsquared threshold"/>
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52
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53 <param name="infoTrack" type="select" label="Add Hapmap information track to image"
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54 help="Refseq genes and snp density can be added to the plot if desired for orientation" >
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55 <option value="info">Add Information track (DISABLED! Awaiting bug fix from Haploview authors since reported in October 2009)</option>
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56 <option value="noinfo" selected="True">No Information track</option>
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57 </param>
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58
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59 <param name="hires" type="select" label="High resolution plots"
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60 help="A high resolution plot file may be possible but only for small regions - not reliable >100's of snps">
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61 <option value="hi">High resolution - only a few (hundreds of) markers</option>
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62 <option value="lo" selected="True">Low resolution - large number of markers</option>
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63 </param>
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64
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65 <param name="memsize" type="select" label="System RAM to allocate"
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66 size="80" help="Very large files will need extra memory (java is a bit of a pig)" >
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67 <option value="1024">1GB</option>
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68 <option value="2048" selected="True">2GB (default)</option>
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69 <option value="4096">4GB</option>
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70 <option value="6144">6GB</option>
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71 <option value="8192">8GB</option>
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72 </param>
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73
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74 </inputs>
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75
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76 <outputs>
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77 <data format="html" name="out_file1" label="${title}.html" />
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78 </outputs>
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79
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80 <!-- python $TOOLPATH/$TOOL.py "" "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \
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81 "$NPRE" $OUTPATH/${NPRE}.html "test" "" "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "hg18" "noinfo" "0.8" \
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82 "['CEU','YRI','CHB+JPT']" $BINPATH/haploview.jar -->
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83 <tests>
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84 <test>
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85 <param name='lhistIn' value='tinywga' ftype='lped' >
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86 <metadata name='base_name' value='tinywga' />
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87 <composite_data value='tinywga.ped' />
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88 <composite_data value='tinywga.map' />
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89 <edit_attributes type='name' value='tinywga' />
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90 </param>
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91 <param name='ucsc_region' value='' />
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92 <param name='title' value='rgHaploViewtest1' />
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93 <param name='rslist' value="rs2283802 rs2267000 rs16997606 rs4820537 rs3788347 rs756632Xrs4820539 rs2283804 rs2267006 rs4822363" />
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94 <param name='ldtype' value='RSQ' />
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95 <param name='minmaf' value='0.0' />
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96 <param name='maxdist' value='200000' />
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97 <param name='tagr2' value='0.8' />
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98 <param name='hmpanel' value="YRI" />
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99 <param name='infoTrack' value='noinfo' />
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100 <param name='hires' value='lo' />
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101 <param name='memsize' value='2048' />
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102 <output name='out_file1' file='rgtestouts/rgHaploView/rgHaploViewtest1.html' ftype='html' lines_diff="60">
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103 <extra_files type="file" name='alljoin.pdf' value="rgtestouts/rgHaploView/alljoin.pdf" compare="sim_size" delta="50000"/>
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104 <extra_files type="file" name='allnup.pdf' value="rgtestouts/rgHaploView/allnup.pdf" compare="sim_size" delta="50000" />
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105 <extra_files type="file" name='Log_rgHaploViewtest1.txt' value="rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt" compare="diff" lines_diff="50"/>
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106 <extra_files type="file" name='rgHaploViewtest1.ped.TESTS' value="rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS" compare="diff"
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107 lines_diff="20"/>
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108 <extra_files type="file" name='rgHaploViewtest1.ped.TAGS' value="rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS" compare="diff"
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109 lines_diff="20" />
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110 </output>
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111 </test>
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112 </tests>
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113
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114 <help>
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115
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116 .. class:: infomark
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117
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118 **Note**
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119
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120 The input file must be in linkage ped format. A suitable file can be chosen from the system library,
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121 or from the files already imported into your current history. Use either one of the selection boxes to
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122 make your choice.
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123
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124 -----
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125
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126 **Syntax**
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127
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128 - **Library Linkage Ped** is a linkage format pedigree file chosen from the system file Library
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129 - **History Linkage Ped** is a linkage format pedigree file chosen from your current Galaxy History
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130 - **Region** is the genomic region cut and paste from a UCSC browser location window
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131 - **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data
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132
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133 -----
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134
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135 **Summary**
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136
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137 This tool is a special purpose tool to estimate and plot linkage disequilibrium estimated
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138 from genotype data in linkage pedigree format (separate map file). All markers in the input file
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139 are used as the default. To limit the calculations to a subset of the input data, supply
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140 a specified genomic region in UCSC browser location format or a list of specific marker IDs.
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141
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142 Note that you can choose either a file of the correct type (linkage pedigree - lped) from
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143 your current history **or** from the system library
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144
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145 This tool currently calls Haploview for estimation and plots. For full attribution, source code and documentation, see
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146 http://www.broad.mit.edu/mpg/haploview/index.php
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147
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148 Copyright, Ross Lazarus, April 2008 for the Rgenetics project
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149 Released under the LGPL. See http://www.gnu.org/licenses/lgpl.html for license terms.
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150
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151 </help>
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152 </tool>
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