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1 <tool id="velvet_test" name="velvet_test" version="3.0 (2013-4-30)">
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2
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3 <macros>
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4 <import>velvet_macro.xml</import>
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5 </macros>
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6 <description>Run velvet or meta-velvetg assembly.</description>
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7
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8 <command interpreter="perl">velvet.pl
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9
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10 $meta
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11
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12 #for $i, $library in enumerate( $shortPaired )
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13
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14 #set $libNumber = $i + 1
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15
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16 #if $libNumber == 1
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17
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18 #set $libNumber = ''
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19
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20 #end if
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21
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22 #if not $library.ins_length.value is None
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23
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24 -ins_length$libNumber $library.ins_length
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25
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26 #end if
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27
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28 #if not $library.ins_length_sd.value is None
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29
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30 -ins_length_sd$libNumber $library.ins_length_sd
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31
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32 #end if
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33
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34 -shortPaired$libNumber
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35
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36 @PAIRED_FILES_OPTIONS@
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37
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38 #end for
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39
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40 #for $i, $library in enumerate( $short )
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41
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42 #set $libNumber = $i + 1
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43
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44 #if $libNumber == 1
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45
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46 #set $libNumber = ''
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47
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48 #end if
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49
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50 -short$libNumber
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51
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52 @UNPAIRED_FILES_OPTIONS@
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53
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54 #end for
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55
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56 #for $i, $library in enumerate( $longPaired )
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57
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58 #if not $library.ins_length.value is None
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59
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60 -ins_length_long $library.ins_length
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61
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62 #end if
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63
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64 #if not $library.ins_length_sd.value is None
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65
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66 -ins_length_long_sd $library.ins_length_sd
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67
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68 #end if
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69
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70 -longPaired
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71
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72 @PAIRED_FILES_OPTIONS@
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73
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74 #end for
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75
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76 #for $i, $library in enumerate( $long )
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77
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78 -long
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79
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80 @UNPAIRED_FILES_OPTIONS@
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81
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82 #end for
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83
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84 #if not $hash_length.value == ''
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85
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86 -hash_length $hash_length
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87
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88 #end if
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89
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90 $strand_specific
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91
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92 #if not $cov_cutoff.value == ''
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93
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94 -cov_cutoff $cov_cutoff
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95
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96 #end if
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97
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98 $read_trkg
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99
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100 #if not $min_contig_lgth.value is None
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101
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102 -min_contig_lgth $min_contig_lgth
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103
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104 #end if
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105
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106 $amos_file
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107
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108 #if not $exp_cov.value == ''
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109
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110 -exp_cov $exp_cov
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111
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112 #end if
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113
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114 #if not $long_cov_cutoff.value == ''
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115
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116 -long_cov_cutoff $long_cov_cutoff
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117
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118 #end if
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119
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120 $scaffolding
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121
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122 #if not $max_branch_length.value is None
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123
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124 -max_branch_length $max_branch_length
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125
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126 #end if
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127
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128 #if not $max_divergence.value is None
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129
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130 -max_divergence $max_divergence
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131
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132 #end if
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133
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134 #if not $max_gap_count.value is None
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135
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136 -max_gap_count $max_gap_count
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137
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138 #end if
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139
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140 #if not $min_pair_count.value is None
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141
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142 -min_pair_count $min_pair_count
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143
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144 #end if
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145
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146 #if not $max_coverage.value is None
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147
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148 -max_coverage $max_coverage
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149
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150 #end if
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151
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152 #if not $coverage_mask.value is None
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153
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154 -coverage_mask $coverage_mask
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155
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156 #end if
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157
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158 #if not $long_mult_cutoff.value is None
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159
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160 -long_mult_cutoff $long_mult_cutoff
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161
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162 #end if
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163
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164 $unused_reads
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165
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166 $alignments
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167
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168 $exportFiltered
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169
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170 #if not $paired_exp_fraction.value is None
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171
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172 -paired_exp_fraction $paired_exp_fraction
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173
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174 #end if
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175
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176 $shortMatePaired
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177
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178 $conserveLong
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179
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180 $discard_chimera
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181
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182 #if not $max_chimera_rate.value is None
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183
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184 -max_chimera_rate $max_chimera_rate
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185
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186 #end if
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187
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188 #if not $repeat_cov_sd.value is None
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189
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190 -repeat_cov_sd $repeat_cov_sd
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191
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192 #end if
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193
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194 #if not $min_split_length.value is None
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195
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196 -min_split_length $min_split_length
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197
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198 #end if
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199
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200 #if not $valid_connections.value is None
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201
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202 -valid_connections $valid_connections
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203
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204 #end if
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205
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206 #if not $noise_connections.value is None
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207
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208 -noise_connections $noise_connections
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209
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210 #end if
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211
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212 $use_connections
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213
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214 $report_split_detail
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215
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216 $report_subgraph
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217
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218 #if not $exp_covs.value == ''
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219
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220 -exp_covs $exp_covs
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221
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222 #end if
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223
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224 #if not $min_peak_cov.value is None
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225
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226 -min_peak_cov $min_peak_cov
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227
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228 #end if
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229
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230 #if not $max_peak_cov.value is None
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231
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232 -max_peak_cov $max_peak_cov
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233
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234 #end if
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235
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236 #if not $histo_bin_width.value is None
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237
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238 -histo_bin_width $histo_bin_width
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239
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240 #end if
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241
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242 #if not $histo_sn_ratio.value is None
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243
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244 -histo_sn_ratio $histo_sn_ratio
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245
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246 #end if
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247
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248 </command>
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249
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250 <inputs>
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251
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252 <param name="hash_length" type="text" value="31" label="Hash length : integer <= 150 OR m,M,s with m (min kmer length) < M (max kmer length) <= 150 and s is a step number"/>
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253
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254 <param name="meta" type="select" label="Perform a metagenomic assembly using meta-velvetg">
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255 <option value="">Yes</option>
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256 <option value="-nometa">No</option>
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257 </param>
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258
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259 <repeat name="shortPaired" max="2" title="Short paired reads library">
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260 <expand macro="paired_library_options" />
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261 </repeat>
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262
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263 <repeat name="short" max="2" title="Short unpaired reads library">
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264 <expand macro="unpaired_library_options" />
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265 </repeat>
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266
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267 <repeat name="longPaired" max="1" title="Long paired reads library">
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268 <expand macro="paired_library_options" />
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269 </repeat>
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270
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271 <repeat name="long" max="1" title="Long unpaired reads library">
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272 <expand macro="unpaired_library_options" />
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273 </repeat>
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274
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275 <param name="reference" type="data" format="fasta" optional="true" label="VELVETH - Reference file (-reference)"/>
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276
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277 <param name="strand_specific" type="select" label="VELVETH - Strand specific transcriptome sequencing data. Default: No (-strand_specific)">
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278 <option value="">No</option>
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279 <option value="-strand_specific">Yes</option>
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280 </param>
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281
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282 <param name="cov_cutoff" type="text" optional="true" label="VELVETG - Coverage cutoff. Float or auto (-cov_cutoff)"/>
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283
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284 <param name="read_trkg" type="select" label="VELVETG - Tracking of short read positions in assembly. Default: no tracking (-read_trkg)">
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285 <option value="">No</option>
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286 <option value="-read_trkg yes">Yes</option>
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287 </param>
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288
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289 <param name="min_contig_lgth" type="integer" optional="true" label="VELVETG - Minimum contig length. Default: hash length * 2 (-min_contig_lgth)"/>
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290
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291 <param name="amos_file" type="select" label="VELVETG - Export assembly to AMOS file. Default: no export (-amos_file)">
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292 <option value="">No</option>
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293 <option value="-amos_file yes">Yes</option>
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294 </param>
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295
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296 <param name="exp_cov" type="text" optional="true" label="VELVETG - Expected coverage of unique regions (float or auto). In case of metagenomic analysis it will be set to auto (-exp_cov)"/>
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297 <param name="long_cov_cutoff" type="text" optional="true" label="VELVETG - Cutoff for removal of nodes with low long-read coverage (-long_cov_cutoff)"/>
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298
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299 <param name="scaffolding" type="select" label="VELVETG - Scaffolding of contigs used paired end information. Default: on (-scaffolding)">
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300 <option value="">Yes</option>
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301 <option value="-scaffolding no">No</option>
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302 </param>
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303
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304 <param name="max_branch_length" type="integer" optional="true" label="VELVETG - Maximum length in base pair of bubble. Default: 100 (-max_branch_length)"/>
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305 <param name="max_divergence" type="float" optional="true" label="VELVETG - Maximum divergence rate between two branches in a bubble. Default: 0.2 (-max_divergence)"/>
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306 <param name="max_gap_count" type="integer" optional="true" label="VELVETG - Maximum number of gaps allowed in the alignment of the two branches of a bubble. Default: 3 (-max_gap_count)"/>
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307 <param name="min_pair_count" type="integer" optional="true" label="VELVETG -Minimum number of paired end connections to justify the scaffolding of two long contigs. Default: 5 (-min_pair_count)"/>
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308
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309 <param name="max_coverage" type="float" optional="true" label="VELVETG - Cutoff for removal of high coverage nodes AFTER tour bus. Default: no removal (-max_coverage)"/>
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310 <param name="coverage_mask" type="integer" optional="true" label="VELVETG - Minimum coverage required for confident regions of contigs. Default: 1 (-coverage_mask)"/>
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311 <param name="long_mult_cutoff" type="integer" optional="true" label="VELVETG -Minimum number of long reads required to merge contigs. Default: 2 (-long_mult_cutoff)"/>
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312
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313 <param name="unused_reads" type="select" label="VELVETG - Export unused reads in UnusedReads.fa file. Default: no (-unused_reads)">
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314 <option value="">No</option>
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315 <option value="-unused_reads yes">Yes</option>
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316 </param>
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317
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318 <param name="alignments" type="select" label="VELVETG - Export a summary of contig alignment to the reference sequences. Default: no (-alignments)">
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319 <option value="">No</option>
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320 <option value="-alignments yes">Yes</option>
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321 </param>
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322
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323 <param name="exportFiltered" type="select" label="VELVETG - Export the long nodes which were eliminated by the coverage filters. Default: no (-exportFiltered)">
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324 <option value="">No</option>
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325 <option value="-exportFiltered yes">Yes</option>
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326 </param>
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327
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328 <param name="paired_exp_fraction" type="float" optional="true" label="VELVETG -Remove all the paired end connections which less than the specified fraction of the expected count. Default: 0.1 (-paired_exp_fraction)"/>
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329
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330 <param name="shortMatePaired" type="select" label="VELVETG - For mate-pair libraries, indicate that the library might be contaminated with paired-end reads. Default no (-shortMatePaired)">
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331 <option value="">No</option>
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332 <option value="-shortMatePaired yes">Yes</option>
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333 </param>
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334
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335 <param name="conserveLong" type="select" label="VELVETG - Preserve sequences with long reads in them. Default no (-conserveLong)">
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336 <option value="">No</option>
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337 <option value="-conserveLong yes">Yes</option>
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338 </param>
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339
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340 <param name="discard_chimera" type="select" label="META-VELVETG - Discard chimera sub-graph. Default: no (-discard_chimera)">
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341 <option value="">No</option>
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342 <option value="-discard_chimera yes">Yes</option>
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343 </param>
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344
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345 <param name="max_chimera_rate" type="float" optional="true" label="META-VELVETG - Maximum allowable chimera rate. Default: 0.0 (-max_chimera_rate)"/>
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346 <param name="repeat_cov_sd" type="float" optional="true" label="META-VELVETG - Standard deviation of repeat node coverages. Default: 0.1 (-repeat_cov_sd)"/>
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347 <param name="min_split_length" type="integer" optional="true" label="META-VELVETG - Minimum node length required for repeat resolution. Default: 0 (-min_split_length)"/>
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348 <param name="valid_connections" type="integer" optional="true" label="META-VELVETG - Minimum allowable number of consistent paired-end connections. Default: 1 (-valid_connections)"/>
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349 <param name="noise_connections" type="integer" optional="true" label="META-VELVETG - Maximum allowable number of inconsistent paired-end connections. Default: 0 (-noise_connections)"/>
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350
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351 <param name="use_connections" type="select" label="META-VELVETG - Use paired-end connections for graph splitting. Default: yes (-use_connections)">
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352 <option value="">Yes</option>
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353 <option value="-use_connections no">No</option>
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354 </param>
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355
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356 <param name="report_split_detail" type="select" label="META-VELVETG - Report sequences around repeat nodes. Default: no (-report_split_detail)">
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357 <option value="">No</option>
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358 <option value="-report_split_detail yes">Yes</option>
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359 </param>
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360
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361 <param name="report_subgraph" type="select" label="META-VELVETG - Report node sequences for each subgraph. Default: no (-report_subgraph)">
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362 <option value="">No</option>
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363 <option value="-report_subgraph yes">Yes</option>
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364 </param>
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365
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366 <param name="exp_covs" type="text" optional="true" label="META-VELVETG - Expected coverages for each species in microbiome. Default: auto (-exp_covs)"/>
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367
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368 <param name="min_peak_cov" type="float" optional="true" label="META-VELVETG - Minimum peak coverage. Default: 0 (-min_peak_cov)"/>
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369 <param name="max_peak_cov" type="float" optional="true" label="META-VELVETG - Maximum peak coverage. Default: 500 (-max_peak_cov)"/>
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370 <param name="histo_bin_width" type="float" optional="true" label="META-VELVETG - Bin width of peak coverage histogram. Default: 1 (-histo_bin_width)"/>
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371 <param name="histo_sn_ratio" type="float" optional="true" label="META-VELVETG - Signal-noise ratio to remove peak noises. Default: 10 (-histo_sn_ratio)"/>
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372
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373 </inputs>
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374
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375 <outputs>
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376
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377 <data format="fasta" name="meta_velvet_contigs" from_work_dir="meta-velvetg.contigs.fa" label="${tool.name} on ${on_string}: meta-velvetg.contigs.fasta">
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378 <filter>(meta == '')</filter>
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379 </data>
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380
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381 <data format="fasta" name="velvet_contigs" from_work_dir="contigs.fa" label="${tool.name} on ${on_string}: contigs.fasta">
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382 <filter>(meta == '-nometa')</filter>
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383 </data>
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384
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385 <data format="fasta" name="velvet_singlets" from_work_dir="Singlets.fasta" label="${tool.name} on ${on_string}: singlets.fasta">
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386 <filter>(unused_reads == '-unused_reads yes')</filter>
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387 </data>
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388
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389 <data format="txt" name="meta-velvetg.asm.afg" from_work_dir="meta-velvetg.asm.afg" label="${tool.name} on ${on_string}: meta-velvetg.asm.afg">
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390 <filter>((meta == '') and (amos_file == '-amos_file yes'))</filter>
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391 </data>
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392
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393 <data format="txt" name="velvet_asm.afg" from_work_dir="velvet_asm.afg" label="${tool.name} on ${on_string}: velvet_asm.afg">
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394 <filter>((meta == '-nometa') and (amos_file == '-amos_file yes'))</filter>
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395 </data>
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396
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397 <data format="tabular" name="stats.txt" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats.txt">
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398 <filter>(meta == '-nometa')</filter>
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399 </data>
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400
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401 <data format="tabular" name="meta-velvetg.split-stats.txt" from_work_dir="meta-velvetg.split-stats.txt" label="${tool.name} on ${on_string}: meta-velvetg.split-stats.txt">
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402 <filter>(meta == '')</filter>
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403 </data>
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404
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405 <data format="txt" name="LastGraph" from_work_dir="LastGraph" label="${tool.name} on ${on_string}: LastGraph">
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406 <filter>(meta == '-nometa')</filter>
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407 </data>
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408
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409 <data format="txt" name="meta-velvetg.LastGraph" from_work_dir="meta-velvetg.LastGraph" label="${tool.name} on ${on_string}: meta-velvetg.LastGraph">
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410 <filter>(meta == '')</filter>
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411 </data>
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412
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413 <data format="tabular" name="meta-velvetg.Graph2-stats.txt" from_work_dir="meta-velvetg.Graph2-stats.txt" label="${tool.name} on ${on_string}: meta-velvetg.Graph2-stats.txt">
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414 <filter>(meta == '')</filter>
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415 </data>
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416
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417 </outputs>
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418
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419 </tool>
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