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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
author Jim Johnson <jj@umn.edu>
date Fri, 21 Oct 2011 11:38:55 -0500
parents
children
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52da588232b0 Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
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1 <tool id="gmap_iit_store" name="GMAP IIT" version="2.0.0">
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2 <description>Create a map store for known genes or SNPs</description>
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3 <requirements>
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4 <requirement type="binary">iit_store</requirement>
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5 <!-- proposed tag for added datatype dependencies -->
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6 <requirement type="datatype">gmap_annotation</requirement>
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7 <requirement type="datatype">gmap_snps</requirement>
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8 <requirement type="datatype">iit</requirement>
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9 <requirement type="datatype">splicesites.iit</requirement>
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10 <requirement type="datatype">introns.iit</requirement>
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11 <requirement type="datatype">snps.iit</requirement>
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12 </requirements>
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13 <version_string>iit_store --version</version_string>
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14 <command interpreter="command"> /bin/bash $shscript 2> $log </command>
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15 <inputs>
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16 <!-- Input data -->
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17 <conditional name="map">
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18 <param name="type" type="select" label="Make map for" >
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19 <option value="genes">Introns and Splice sites</option>
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20 <option value="snps">SNPs</option>
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21 <option value="gmap">GMAP Annotation</option>
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22 </param>
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23 <when value="genes">
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24 <conditional name="src">
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25 <param name="src_format" type="select" label="Add splice and intron info from" >
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26 <option value="refGeneTable">refGenes table from UCSC table browser</option>
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27 <option value="gtf">GTF</option>
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28 <option value="gff3">GFF3</option>
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29 </param>
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30 <when value="refGeneTable">
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31 <param name="genes" type="data" format="tabular" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" />
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32 <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)"
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33 help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">
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34 <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>
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35 </param>
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36 </when>
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37 <when value="gtf">
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38 <param name="genes" type="data" format="gtf" label="Genes as GTF" help="" />
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39 </when>
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40 <when value="gff3">
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41 <param name="genes" type="data" format="gff3" label="Genes in GFF3 format" help="" />
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42 </when>
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43 </conditional>
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44 <param name="maps" type="select" display="checkboxes" multiple="true" force_select="true" label="Add splice and intron info from" >
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45 <option value="splicesites" selected="true">splicesites.iit</option>
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46 <option value="introns" selected="false">introns.iit</option>
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47 </param>
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48 </when>
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49 <when value="snps">
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50 <conditional name="src">
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51 <param name="src_format" type="select" label="Add SNP info from" >
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52 <option value="snpTable">UCSC SNP Table</option>
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53 <option value="snpFile">GMAP SNP File</option>
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54 </param>
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55 <when value="snpTable">
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56 <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
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57 <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" />
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58 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
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59 <option value="1" selected="true">1 (High)</option>
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60 <option value="2">2 (Medium)</option>
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61 <option value="3">3 (All)</option>
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62 </param>
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63 </when>
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64 <when value="snpFile">
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65 <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file"
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66 help="Format (3 columns):&lt;B&gt;
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67 &lt;br&gt;>rs62211261 21:14379270 CG
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68 &lt;br&gt;>rs62211262 21:14379281 CG
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69 &lt;/B&gt;
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70 &lt;br&gt;Each line must start with a &gt; character, then be followed by an
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71 identifier (which may have duplicates). Then there should be the
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72 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so
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73 the first character of a chromosome is number 1.) Finally, there
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74 should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN)
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75 &lt;br&gt;These alleles must correspond to the possible nucleotides on the plus strand of the genome.
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76 If the one of these two letters does not match the allele in the reference
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77 sequence, that SNP will be ignored in subsequent processing as a probable error.
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78 The N stands for any other allele." />
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79 </when>
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80 </conditional>
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81 </when>
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82 <when value="gmap">
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83 <param name="annotation" type="data" format="gmap_annotation" label="GMAP mapfile"
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84 help="Format (2 or columns): &lt;B&gt;
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85 &lt;br&gt;>label coords optional_tag
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86 &lt;br&gt;optional_annotation (which may be zero, one, or multiple lines)
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87 &lt;/B&gt;
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88 &lt;br&gt;Each line must start with a &gt; character, then be followed by an identifier (which may have duplicates).
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89 &lt;br&gt;Then there should be the chromosomal coordinate range. (Coordinates are all 1-based, so the first character of a chromosome is number 1.)
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90 &lt;br&gt;The coords should be of the form
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91 &lt;br&gt; chr:position
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92 &lt;br&gt; chr:startposition..endposition
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93 &lt;br&gt;The term chr:position is equivalent to chr:position..position.
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94 &lt;br&gt;If you want to indicate that the interval is on the minus strand or reverse direction, then endposition may be less than startposition.
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95 " />
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96 </when>
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97 </conditional>
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98 </inputs>
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99 <outputs>
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100 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
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101 <data format="splicesites.iit" name="splicesites_iit" label="${tool.name} on ${on_string} splicesites.iit">
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102 <filter>(map['type'] == 'genes' and 'splicesites' in map['maps'])</filter>
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103 </data>
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104 <data format="introns.iit" name="introns_iit" label="${tool.name} on ${on_string} introns.iit">
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105 <filter>(map['type'] == 'genes' and 'introns' in map['maps'])</filter>
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106 </data>
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107 <data format="snps.iit" name="snps_iit" label="${tool.name} on ${on_string} snps.iit">
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108 <filter>(map['type'] == 'snps')</filter>
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109 </data>
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110 <data format="iit" name="map_iit" label="${tool.name} on ${on_string} map.iit">
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111 <filter>(map['type'] == 'gmap')</filter>
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112 </data>
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113 </outputs>
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114 <configfiles>
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115 <configfile name="shscript">
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116 #!/bin/bash
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117 #set $catcmd = 'gzcat -f'
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118 #set $catcmd = 'cat'
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119 #set $ds = chr(36)
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120 #set $gt = chr(62)
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121 #set $lt = chr(60)
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122 #set $ad = chr(38)
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123 #set $ep = chr(33)
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124 #set $toerr = ''.join([$gt,$ad,'2'])
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125 #import os.path
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126 #if $map.type == 'genes':
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127 if [ $ep -e $map.src.genes ]; then echo "$map.src.genes does not exist" $toerr; exit 1; fi
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128 if [ $ep -s $map.src.genes ]; then echo "$map.src.genes is empty" $toerr; exit 2; fi
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129 #if $map.src.src_format == 'refGeneTable':
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130 #if 'splicesites' in [ $map.maps.__str__ ]:
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131 $catcmd $map.src.genes | psl_splicesites -s $map.src.col_skip | iit_store -o $splicesites_iit
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132 #end if
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133 #if 'introns' in [ $map.maps.__str__ ]:
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134 $catcmd $map.src.genes | psl_introns -s $map.src.col_skip | iit_store -o $introns_iit
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135 #end if
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136 #elif $map.src.src_format == 'gtf':
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137 #if 'splicesites' in [ $map.maps.__str__ ]:
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138 $catcmd $map.src.genes | gtf_splicesites | iit_store -o $splicesites_iit
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139 #end if
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140 #if 'introns' in [ $map.maps.__str__ ]:
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141 $catcmd $map.src.genes | gtf_introns | iit_store -o $introns_iit
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142 #end if
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143 #elif $map.src.src_format == 'gff3':
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144 #if 'splicesites' in [ $map.maps.__str__ ]:
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145 $catcmd $map.src.genes | gff3_splicesites | iit_store -o $splicesites_iit
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146 #end if
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147 #if 'introns' in [ $map.maps.__str__ ]:
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148 $catcmd $map.src.genes | gff3_introns | iit_store -o $introns_iit
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149 #end if
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150 #end if
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151 #elif $map.type == 'snps':
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152 if [ $ep -s $map.src.snps ]; then echo "$map.src.snps is empty" $toerr; exit 2; fi
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153 #if $map.src.snpsex.__str__ != 'None':
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154 $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight -e $map.src.snpsex | iit_store -o $snps_iit
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155 #else:
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156 $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight | iit_store -o $snps_iit
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157 #end if
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158 #else:
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159 $catcmd $map.src.snps | iit_store -o $map_iit
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160 #end if
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161 </configfile>
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162 </configfiles>
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163
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164 <tests>
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165 </tests>
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166
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167 <help>
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168
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169
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170 **iit_store**
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171
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172 GMAP IIT creates an Interval Index Tree map of known splice sites, introns, or SNPs (it uses iit_store described in the GMAP documentation). The maps can be used in GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). Maps are typically used for known splice sites, introns, or SNPs.
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173
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174 You will want to read the README_
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175
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176 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
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177
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178 .. _GMAP: http://research-pub.gene.com/gmap/
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179 .. _GSNAP: http://research-pub.gene.com/gmap/
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180 .. _README: http://research-pub.gene.com/gmap/src/README
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181 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
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182
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183
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184 **inputs**
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185
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186 </help>
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187 </tool>
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188