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1 <tool id="gmap_build" name="GMAP Build" version="2.0.0">
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2 <description>a database genome index for GMAP and GSNAP</description>
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3 <requirements>
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4 <requirement type="package" version="2011-11-30">gmap</requirement>
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5 </requirements>
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6 <version_string>gmap --version</version_string>
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7 <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>
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8 <inputs>
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9 <!-- Name for this gmapdb -->
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10 <param name="refname" type="text" label="Name you want to give this gmap database" help="">
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11 <validator type="empty_field" message="A database name is required."/>
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12 </param>
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13 <!-- Input data -->
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14 <repeat name="inputs" title="Reference Sequence" min="1">
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15 <param name="input" type="data" format="fasta" label="reference sequence fasta" />
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16 </repeat>
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17
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18 <param name="kmer" type="select" multiple="true" force_select="true" label="kmer size" help="">
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19 <option value="12">12</option>
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20 <option value="13">13</option>
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21 <option value="14">14</option>
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22 <option value="15" selected="true">15</option>
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23 </param>
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24 <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/>
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25 <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/>
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26 <conditional name="splicesite">
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27 <param name="splice_source" type="select" label="Add splice and intron info from" >
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28 <option value="none"></option>
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29 <option value="refGeneTable">refGenes table from UCSC table browser</option>
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30 <option value="gtf">GTF</option>
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31 <option value="gff3">GFF3</option>
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32 </param>
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33 <when value="none"/>
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34 <when value="refGeneTable">
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35 <param name="refGenes" type="data" format="tabular" optional="true" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" />
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36 <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)"
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37 help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">
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38 <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>
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39 </param>
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40
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41 </when>
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42 <when value="gtf">
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43 <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" />
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44 </when>
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45 <when value="gff3">
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46 <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" />
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47 </when>
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48 </conditional>
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49 <conditional name="dbsnp">
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50 <param name="snp_source" type="select" label="Add SNP info from" >
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51 <option value="none"></option>
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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="none"/>
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56 <when value="snpTable">
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57 <param name="snps" type="data" format="tabular" optional="true" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
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58 <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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59 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
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60 <option value="1" selected="true">1 (High)</option>
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61 <option value="2">2 (Medium)</option>
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62 <option value="3">3 (All)</option>
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63 </param>
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64 </when>
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65 <when value="snpFile">
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66 <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file"
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67 help="Format (3 columns):
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68 <br>>rs62211261 21:14379270 CG
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69 <br>>rs62211262 21:14379281 CG
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70 <br>Each line must start with a > 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 <br>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 </inputs>
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82 <outputs>
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83 <!--
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84 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
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85 -->
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86 <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" />
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87 </outputs>
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88 <configfiles>
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89 <configfile name="shscript">
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90 #!/bin/bash
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91 #set $ds = chr(36)
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92 #set $gt = chr(62)
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93 #set $lt = chr(60)
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94 #set $ad = chr(38)
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95 ## #set $ref_files = ''
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96 ## #for $i in $inputs:
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97 ## #set $ref_files = $ref_files $i.input
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98 ## #end for
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99 ## echo $ref_files
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100 #import os.path
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101 #set $gmapdb = $output.extra_files_path
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102 #set $mapsdir = $os.path.join($os.path.join($gmapdb,str($refname)), str($refname) + '.maps')
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103 mkdir -p $gmapdb
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104 ## export GMAPDB required for cmetindex and atoiindex
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105 export GMAPDB=$gmapdb
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106 #for $k in $kmer.__str__.split(','):
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107 gmap_build -D $gmapdb -d $refname -s numeric-alpha -k $k #for i in $inputs# ${i.input}#end for#
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108 #end for
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109 get-genome -D $gmapdb -d '?' | sed 's/^Available .*/gmap db: /'
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110 echo "kmers: " $kmer
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111 #if $splicesite.splice_source == 'refGeneTable':
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112 #if $splicesite.refGenes.__str__ != 'None':
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113 cat $splicesite.refGenes | psl_splicesites -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,'splicesites')
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114 cat $splicesite.refGenes | psl_introns -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,'introns')
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115 #end if
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116 #elif $splicesite.splice_source == 'gtf':
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117 #if $splicesite.gtfGenes.__str__ != 'None':
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118 cat $splicesite.gtfGenes | gtf_splicesites | iit_store -o $os.path.join($mapsdir,'splicesites')
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119 cat $splicesite.gtfGenes | gtf_introns | iit_store -o $os.path.join($mapsdir,'introns')
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120 #end if
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121 #elif $splicesite.splice_source == 'gff3':
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122 #if $splicesite.gff3Genes.__str__ != 'None':
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123 cat $splicesite.gff3Genes | gff3_splicesites | iit_store -o $os.path.join($mapsdir,'splicesites')
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124 cat $splicesite.gff3Genes | gff3_introns | iit_store -o $os.path.join($mapsdir,'introns')
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125 #end if
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126 #end if
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127 #if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None':
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128 #if $dbsnp.snp_source == 'snpTable':
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129 #if $dbsnp.snpsex.__str__ != 'None':
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130 cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex | iit_store -o $os.path.join($mapsdir,'snps')
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131 #else:
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132 cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o $os.path.join($mapsdir,'snps')
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133 #end if
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134 #else:
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135 cat $dbsnp.snps | iit_store -o $os.path.join($mapsdir,'snps')
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136 #end if
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137 snpindex -d $refname -v snps
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138 echo "snpindex" -d $refname -v snps
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139 #end if
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140 #if $cmetindex.__str__ == 'yes':
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141 cmetindex -d $refname
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142 echo "cmetindex" -d $refname
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143 #end if
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144 #if $atoiindex.__str__ == 'yes':
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145 atoiindex -d $refname
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146 echo "atoiindex" -d $refname
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147 #end if
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148 get-genome -D $gmapdb -d $refname -m '?' | sed 's/^Available maps .*/maps: /'
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149 </configfile>
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150 </configfiles>
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151
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152 <tests>
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153 </tests>
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154
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155 <help>
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156
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157
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158 **GMAP Build**
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159
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160 GMAP Build creates an index of a genomic sequence for mapping and alignment using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). (GMAP Build uses GMSP commands: gmap_build, iit_store, psl_splicesites, psl_introns, gtf_splicesites, gtf_introns, gff3_splicesites, gff3_introns, dbsnp_iit, snpindex, cmetindex, and atoiindex.)
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161
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162 You will want to read the README_
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163
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164 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
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165
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166 .. _GMAP: http://research-pub.gene.com/gmap/
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167 .. _GSNAP: http://research-pub.gene.com/gmap/
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168 .. _README: http://research-pub.gene.com/gmap/src/README
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169 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
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170
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171
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172 </help>
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173 </tool>
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174
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