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1 <tool id="gmap" name="GMAP" version="2.0.1">
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2 <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description>
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3 <requirements>
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4 <requirement type="binary">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>
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8 #import os,os.path
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9 gmap
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10 --nthreads=4 --ordered
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11 #if $refGenomeSource.genomeSource == "history":
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12 --gseg=$refGenomeSource.ownFile
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13 #elif $refGenomeSource.genomeSource == "gmapdb":
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14 #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0]
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15 --dir=$refGenomeSource.gmapdb.extra_files_path --db=$gmapdb
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16 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:
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17 --kmer=$refGenomeSource.kmer
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18 #end if
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19 #else:
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20 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)
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21 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:
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22 --kmer=$refGenomeSource.kmer
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23 #end if
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24 #end if
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25 #if $result.format == "summary":
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26 --summary
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27 #elif $result.format == "align":
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28 --align
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29 #elif $result.format == "continuous":
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30 --continuous
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31 #elif $result.format == "continuous-by-exon":
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32 --continuous-by-exon
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33 #elif $result.format == "compress":
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34 --compress
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35 #elif $result.format == "exons_dna":
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36 --exons=cdna
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37 #elif $result.format == "exons_gen":
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38 --exons=genomic
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39 #elif $result.format == "protein_dna":
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40 --protein_dna
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41 #elif $result.format == "protein_gen":
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42 --protein_gen
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43 #elif $result.format == "sam":
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44 --format=$result.sam_paired_read
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45 $result.no_sam_headers
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46 #* Removed in gmap version 2011-11-30
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47 #if len($result.noncanonical_splices.__str__) > 0
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48 --noncanonical-splices=$result.noncanonical_splices
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49 #end if
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50 *#
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51 #if len($result.read_group_id.__str__) > 0
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52 --read-group-id=$result.read_group_id
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53 #end if
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54 #if len($result.read_group_name.__str__) > 0
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55 --read-group-name=$result.read_group_name
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56 #end if
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57 #if len($result.read_group_library.__str__) > 0
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58 --read-group-library=$result.read_group_library
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59 #end if
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60 #if len($result.read_group_platform.__str__) > 0
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61 --read-group-platform=$result.read_group_platform
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62 #end if
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63 #elif $result.format != "gmap":
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64 --format=$result.format
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65 #end if
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66 #if $computation.options == "advanced":
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67 $computation.nosplicing
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68 $computation.cross_species
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69 #if len($computation.min_intronlength.__str__) > 0
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70 --min-intronlength=$computation.min_intronlength
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71 #end if
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72 #if len($computation.intronlength.__str__) > 0
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73 --intronlength=$computation.intronlength
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74 #end if
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75 #if len($computation.localsplicedist.__str__) > 0
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76 --localsplicedist=$computation.localsplicedist
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77 #end if
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78 #if len($computation.totallength.__str__) > 0
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79 --totallength=$computation.totallength
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80 #end if
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81 #if len($computation.trimendexons.__str__) > 0
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82 --trimendexons=$computation.trimendexons
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83 #end if
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84 --direction=$computation.direction
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85 --canonical-mode=$computation.canonical
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86 --prunelevel=$computation.prunelevel
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87 --allow-close-indels=$computation.allow_close_indels
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88 #if len($computation.microexon_spliceprob.__str__) >= 0:
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89 --microexon-spliceprob=$computation.microexon_spliceprob
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90 #end if
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91 #if len($computation.chimera_margin.__str__) >= 0:
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92 --chimera-margin=$computation.chimera_margin
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93 #end if
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94 #end if
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95 #if $advanced.options == "used":
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96 #if len($advanced.npaths.__str__) > 0:
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97 --npaths=$advanced.npaths
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98 #end if
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99 #if len($advanced.suboptimal_score.__str__) > 0:
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100 --suboptimal-score=$advanced.suboptimal_score
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101 #end if
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102 #if len($advanced.chimera_overlap.__str__) > 0:
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103 --chimera_overlap=$advanced.chimera_overlap
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104 #end if
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105 $advanced.protein
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106 $advanced.tolerant
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107 $advanced.nolengths
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108 $advanced.invertmode
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109 #if len($advanced.introngap.__str__) > 0:
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110 --introngap=$advanced.introngap
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111 #end if
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112 #if len($advanced.wraplength.__str__) > 0:
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113 --wraplength=$advanced.wraplength
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114 #end if
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115 #end if
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116 #if $split_output == True
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117 $split_output
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118 #end if
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119 #if len($quality_protocol.__str__) > 0:
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120 --quality-protocol=$quality_protocol
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121 #end if
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122 $input
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123 #for $i in $inputs:
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124 ${i.added_input}
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125 #end for
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126 #if $split_output == True
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127 2> $gmap_stderr
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128 #else
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129 2> $gmap_stderr > $output
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130 #end if
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131 </command>
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132 <inputs>
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133 <!-- Input data -->
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134 <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="<H2>Input Sequences</H2>Select an mRNA or EST dataset to map" />
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135 <repeat name="inputs" title="addtional mRNA or EST dataset to map">
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136 <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/>
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137 </repeat>
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138 <param name="quality_protocol" type="select" label="Protocol for input quality scores">
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139 <option value="">No quality scores</option>
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140 <option value="sanger">Sanger quality scores</option>
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141 <option value="illumina">Illumina quality scores</option>
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142 </param>
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143
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144 <!-- GMAPDB for mapping -->
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145 <conditional name="refGenomeSource">
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146 <param name="genomeSource" type="select" label="<HR><H2>Map To</H2>Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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147 <option value="indexed">Use a built-in index</option>
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148 <option value="gmapdb">Use gmapdb from the history</option>
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149 <option value="history">Use a fasta reference sequence from the history</option>
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150 </param>
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151 <when value="indexed">
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152 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
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153 <options from_file="gmap_indices.loc">
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154 <column name="uid" index="0" />
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155 <column name="dbkey" index="1" />
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156 <column name="name" index="2" />
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157 <column name="kmers" index="3" />
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158 <column name="maps" index="4" />
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159 <column name="snps" index="5" />
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160 <column name="value" index="6" />
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161 </options>
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162 </param>
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163 <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size">
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164 <options from_file="gmap_indices.loc">
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165 <column name="name" index="3"/>
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166 <column name="value" index="3"/>
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167 <filter type="param_value" ref="gmapindex" column="6"/>
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168 <filter type="multiple_splitter" column="3" separator=","/>
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169 <filter type="add_value" name="" value=""/>
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170 <filter type="sort_by" column="3"/>
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171 </options>
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172 </param>
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173 <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" help="">
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174 <options from_file="gmap_indices.loc">
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175 <column name="name" index="4"/>
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176 <column name="value" index="4"/>
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177 <filter type="param_value" ref="gmapindex" column="6"/>
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178 <filter type="multiple_splitter" column="4" separator=","/>
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179 <filter type="add_value" name="" value=""/>
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180 <filter type="sort_by" column="4"/>
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181 </options>
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182 </param>
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183 </when>
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184 <when value="gmapdb">
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185 <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb"
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186 help="A GMAP database built with GMAP Build"/>
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187 <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size">
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188 <options>
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189 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/>
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190 </options>
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191 </param>
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192 <param name="map" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help="">
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193 <options>
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194 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/>
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195 </options>
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196 </param>
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197 </when>
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198 <when value="history">
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199 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome"
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200 help="Fasta containing genomic DNA sequence"/>
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201 </when>
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202 </conditional>
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203
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204
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205 <!-- Computation options -->
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206 <conditional name="computation">
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207 <param name="options" type="select" label="<HR>Computational Settings" help="">
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208 <option value="default">Use default settings</option>
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209 <option value="advanced">Set Computation Options</option>
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210 </param>
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211 <when value="default"/>
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212 <when value="advanced">
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213 <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/>
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214 <param name="min_intronlength" type="integer" value="" optional="true" label="Min length for one internal intron (default 9)." help="Below this size, a genomic gap will be considered a deletion rather than an intron." >
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215 <validator type="in_range" message="min_intronlength must be positive" min="0" />
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216 </param>
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217 <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" >
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218 <validator type="in_range" message="intronlength must be positive" min="0" />
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219 </param>
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220 <param name="localsplicedist" type="integer" value="" optional="true" label="Max length for known splice sites at ends of sequence (default 200000)" >
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221 <validator type="in_range" message="localsplicedist must be positive" min="0" />
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222 </param>
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223 <param name="totallength" type="integer" value="" optional="true" label="Max total intron length (default 2400000)" >
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224 <validator type="in_range" message="totallength must be positive" min="0" />
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225 </param>
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226 <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera"
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227 help=" default is 40, To turn off, set to a large value (greater than the query length)" >
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228 <validator type="in_range" message="chimera_margin must be positive" min="0" />
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229 </param>
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230 <param name="direction" type="select" label="cDNA direction">
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231 <option value="auto">auto</option>
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232 <option value="sense_force">sense_force</option>
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233 <option value="antisense_force">antisense_force</option>
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234 <option value="sense_filter">sense_filter</option>
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235 <option value="antisense_filter">antisense_filter</option>
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236 </param>
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237 <param name="trimendexons" type="integer" value="" optional="true" label="Trim end exons with fewer than given number of matches (in nt, default 12)" >
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238 <validator type="in_range" message="trimendexons must be positive" min="1" />
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239 </param>
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240 <param name="cross_species" type="boolean" truevalue="--cross-species" falsevalue="" checked="false" label="Cross-species alignment" help="For cross-species alignments, use a more sensitive search for canonical splicing"/>
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241
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242 <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns">
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243 <option value="1">high reward (default)</option>
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244 <option value="0">low reward</option>
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245 <option value="2">low reward for high-identity sequences</option>
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246 </param>
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247 <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other">
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248 <option value="1" selected="true">yes (default)</option>
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249 <option value="0">no</option>
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250 <option value="2">only for high-quality alignments</option>
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251 </param>
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252 <param name="microexon_spliceprob" type="float" value="" optional="true" label="Micro Exon splice probablility threshold"
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253 help="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" >
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254 <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/>
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255 </param>
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256 <param name="prunelevel" type="select" label="Pruning level">
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257 <option value="0">no pruning (default)</option>
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258 <option value="1">poor sequences</option>
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259 <option value="2">repetitive sequences</option>
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260 <option value="3">poor and repetitive sequences</option>
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261 </param>
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262 <!-- could do this as a config file
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263 <param name="chrsubsetfile" type="data" format="fasta" label="User-supplied chromosome subset file" />
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264 <param name="chrsubset" type="text" label="Chromosome subset to search" />
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265 -->
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266 </when>
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267 </conditional>
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268
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269 <!-- Advanced Settings -->
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270 <conditional name="advanced">
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271 <param name="options" type="select" label="<HR>Advanced Settings" help="">
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272 <option value="default">Use default settings</option>
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273 <option value="used">Set Options</option>
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274 </param>
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275 <when value="default"/>
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276 <when value="used">
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277 <param name="nolengths" type="boolean" checked="false" truevalue="--nolengths=true" falsevalue="" label="No intron lengths in alignment"/>
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278 <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help="">
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279 <option value="">Don't invert the cDNA (default)</option>
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280 <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option>
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281 <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option>
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282 </param>
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283 <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)">
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284 <validator type="in_range" message="introngap must be positive" min="0" />
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285 </param>
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286 <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)">
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287 <validator type="in_range" message="wraplength must be positive" min="1" />
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288 </param>
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289 <param name="npaths" type="integer" value="" optional="true"
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290 label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." >
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291 <validator type="in_range" message="npaths must be positive" min="0" />
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292 </param>
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293 <param name="suboptimal_score" type="integer" value="" optional="true"
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294 label="Report only paths whose score is within this value of the best path"
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295 help="By default the program prints all paths found." >
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296 <validator type="in_range" message="suboptimal_score must be positive" min="0" />
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297 </param>
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298 <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" >
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299 <validator type="in_range" message="chimera_overlap must be positive" min="0" />
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300 </param>
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301 <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue=""
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302 label="Translates cDNA with corrections for frameshifts"/>
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303 <param name="protein" type="select" label="Protein alignment" help="">
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304 <option value="">default</option>
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305 <option value="--fulllength=true">Assume full-length protein, starting with Met</option>
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306 <option value="--truncate=true">Truncate alignment around full-length protein, Met to Stop</option>
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307 </param>
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308 </when>
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309 </conditional>
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310
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311 <!-- Output data -->
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312 <conditional name="result">
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313 <param name="format" type="select" label="<HR><H2>Output</H2>Select the output format" help="">
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314 <option value="gmap">GMAP default output</option>
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315 <option value="summary">Summary of alignments</option>
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316 <option value="align">Alignment</option>
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317 <option value="continuous">Alignment in three continuous lines</option>
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318 <option value="continuous-by-exon">Alignment in three lines per exon</option>
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319 <option value="compress">Print output in compressed format</option>
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320 <option value="exons_dna">Print exons cDNA</option>
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321 <option value="exons_gen">Print exons genomic</option>
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322 <option value="protein_dna">Print protein sequence (cDNA)</option>
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323 <option value="protein_gen">Print protein sequence (genomic)</option>
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324 <option value="psl">PSL (BLAT) format</option>
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325 <option value="gff3_gene">GFF3 gene format</option>
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326 <option value="gff3_match_cdna">GFF3 match cDNA format</option>
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327 <option value="gff3_match_est">GFF3 match EST format</option>
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328 <option value="splicesites">splicesites output (for GSNAP)</option>
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329 <option value="introns">introns output (for GSNAP)</option>
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330 <option value="map_exons">IIT FASTA exon map format</option>
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331 <option value="map_genes">IIT FASTA map format</option>
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332 <option value="coords">coords in table format</option>
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333 <option value="sam" selected="true">SAM format</option>
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334 </param>
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335 <when value="gmap">
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336 </when>
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337 <when value="summary"/>
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338 <when value="align">
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339 </when>
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340 <when value="continuous">
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341 </when>
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342 <when value="continuous-by-exon">
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343 </when>
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344 <when value="compress"/>
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345 <when value="exons_dna"/>
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346 <when value="exons_gen"/>
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347 <when value="protein_dna"/>
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348 <when value="protein_gen"/>
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349 <when value="psl"/>
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350 <when value="gff3_gene"/>
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351 <when value="gff3_match_cdna"/>
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352 <when value="gff3_match_est"/>
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353 <when value="splicesites"/>
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354 <when value="introns"/>
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355 <when value="map_exons"/>
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356 <when value="map_genes"/>
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357 <when value="coords"/>
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358 <when value="sam">
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359 <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/>
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360 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/>
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361 <!-- Removed in gmap version 2011-11-30
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362 <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING.">
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363 <option value="">Use default</option>
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364 <option value="N">N</option>
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365 <option value="D">D</option>
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366 </param>
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367 -->
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368 <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/>
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369 <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/>
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370 <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/>
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371 <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/>
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372 </when>
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373 </conditional> <!-- name="result" -->
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374
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375 <param name="split_output" type="boolean" truevalue="--split-output=gmap_out" falsevalue="" checked="false" label="Separate outputs for nomapping, uniq, mult, and chimera" help="(chimera only when chimera-margin is selected)"/>
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376
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377
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378 <!--
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379 map=iitfile Map file. If argument is '?' (with the quotes), this lists available map files.
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380 mapexons Map each exon separately
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381 mapboth Report hits from both strands of genome
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382 flanking=INT Show flanking hits (default 0)
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383 print-comment Show comment line for each hit
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384 -->
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385
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386
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387 </inputs>
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388 <outputs>
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389 <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/>
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390 <data format="txt" name="output" label="${tool.name} on ${on_string} ${result.format}" >
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391 <filter>(split_output == False)</filter>
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392 <change_format>
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393 <when input="result['format']" value="gff3_gene" format="gff3"/>
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394 <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
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395 <when input="result['format']" value="gff3_match_est" format="gff3"/>
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396 <when input="result['format']" value="sam" format="sam"/>
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397 <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
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398 <when input="result['format']" value="introns" format="gmap_introns"/>
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399 <when input="result['format']" value="map_genes" format="gmap_annotation"/>
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400 <when input="result['format']" value="map_exons" format="gmap_annotation"/>
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401 </change_format>
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402 </data>
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403 <data format="txt" name="uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gmap_out.uniq">
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404 <filter>(split_output == True)</filter>
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405 <change_format>
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406 <when input="result['format']" value="gff3_gene" format="gff3"/>
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407 <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
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408 <when input="result['format']" value="gff3_match_est" format="gff3"/>
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409 <when input="result['format']" value="sam" format="sam"/>
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410 <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
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411 <when input="result['format']" value="introns" format="gmap_introns"/>
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412 <when input="result['format']" value="map_genes" format="gmap_annotation"/>
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413 <when input="result['format']" value="map_exons" format="gmap_annotation"/>
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414 </change_format>
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415 </data>
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416 <data format="txt" name="transloc" label="${tool.name} on ${on_string} transloc.${result.format}" from_work_dir="gmap_out.transloc">
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417 <filter>(split_output == True)</filter>
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418 <change_format>
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419 <when input="result['format']" value="gff3_gene" format="gff3"/>
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420 <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
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421 <when input="result['format']" value="gff3_match_est" format="gff3"/>
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422 <when input="result['format']" value="sam" format="sam"/>
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423 <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
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424 <when input="result['format']" value="introns" format="gmap_introns"/>
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425 <when input="result['format']" value="map_genes" format="gmap_annotation"/>
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426 <when input="result['format']" value="map_exons" format="gmap_annotation"/>
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427 </change_format>
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428 </data>
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429 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gmap_out.nomapping">
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430 <filter>(split_output == True)</filter>
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431 <change_format>
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432 <when input="result['format']" value="gff3_gene" format="gff3"/>
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433 <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
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434 <when input="result['format']" value="gff3_match_est" format="gff3"/>
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435 <when input="result['format']" value="sam" format="sam"/>
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436 <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
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437 <when input="result['format']" value="introns" format="gmap_introns"/>
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438 <when input="result['format']" value="map_genes" format="gmap_annotation"/>
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439 <when input="result['format']" value="map_exons" format="gmap_annotation"/>
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440 </change_format>
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441 </data>
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442 <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}" from_work_dir="gmap_out.mult">
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443 <filter>(split_output == True)</filter>
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444 <change_format>
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445 <when input="result['format']" value="gff3_gene" format="gff3"/>
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446 <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
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447 <when input="result['format']" value="gff3_match_est" format="gff3"/>
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448 <when input="result['format']" value="sam" format="sam"/>
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449 <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
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450 <when input="result['format']" value="introns" format="gmap_introns"/>
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451 <when input="result['format']" value="map_genes" format="gmap_annotation"/>
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452 <when input="result['format']" value="map_exons" format="gmap_annotation"/>
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453 </change_format>
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454 </data>
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455 </outputs>
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456 <tests>
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457 </tests>
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458
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459 <help>
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460
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461 **What it does**
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462
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463 GMAP_ (Genomic Mapping and Alignment Program) The functionality provided by gmap allows a user to: (1) map and align a single cDNA interactively against a large genome in about a second, without the startup time of several minutes typically needed by existing mapping programs; (2) switch arbitrarily among different genomes, without the need for a preloaded server dedicated to each genome; (3) run the program on computers with as little as 128 MB of RAM (random access memory); (4) perform high-throughput batch processing of cDNAs by using memory mapping and multithreading when appropriate memory and hardware are available; (5) generate accurate gene models, even in the presence of substantial polymorphisms and sequence errors; (6) locate splice sites accurately without the use of probabilistic splice site models, allowing generalized use of the program across species; (7) detect statistically significant microexons and incorporate them into the alignment; and (8) handle mapping and alignment tasks on genomes having alternate assemblies, linkage groups or strains. It is developed by Thomas D. Wu of Genentech, Inc.
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464
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465 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
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466
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467 .. _GMAP: http://research-pub.gene.com/gmap/
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468 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
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469
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470 ------
|
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471
|
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472 **Know what you are doing**
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473
|
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474 .. class:: warningmark
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475
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476 You will want to read the README_
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477
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478 .. _README: http://research-pub.gene.com/gmap/src/README
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479
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480 </help>
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481 </tool>
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482
|
