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1 <tool id="novocraft_wrapper" name="Novocraft" version="3.00.02">
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2 <description>maps query reads onto the reference sequences</description>
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3 <command interpreter="python">
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4 novocraft_wrapper.py
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5 ## Parameters
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6 --settings=$params.settingsType
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7 #if $params.settingsType == "full":
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8 --align=${params.t}
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9 --open=${params.g}
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10 --extend=${params.x}
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11 --trunc=${params.n}
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12 --kmer=${params.k}
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13 --step=${params.s}
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14 --qual=${params.l}
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15 --repe=${params.m}
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16 --hclip=${params.H}
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17 --pam=$params.pairedEnd
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18 --sd=${params.d}
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19 --insert=${params.i}
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20 #end if
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21
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22 #if $genomeSource.refGenomeSource == "history":
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23 ##build index on the fly
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24 --refer="${genomeSource.refFile}"
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25 ##--dbkey=$dbkey
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26 #else:
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27 ##use precomputed indexes
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28 --ref1="${genomeSource.indices.fields.path}"
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29 ##--do_not_build_index
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30 #end if
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31
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32 ## input file(s)
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33 --input1=$paired.input1
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34 #if $paired.sPaired == "paired":
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35 --input2=$paired.input2
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36 #end if
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37
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38 ## Outputs.
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39 --output=$output
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40
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41 </command>
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42 <inputs>
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43 <conditional name="genomeSource">
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44 <param name="refGenomeSource" type="select" label="Select a reference genome from your history or use a built-in index?">
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45 <option value="indexed">Use a built-in index</option>
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46 <option value="history">Use one from the history</option>
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47 </param>
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48
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49 <when value="indexed">
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50 <param name="indices" type="select" label="Select a reference genome">
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51 <options from_data_table="novocraft_indexes">
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52 <filter type="sort_by" column="2" />
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53 <validator type="no_options" message="No indexes are available" />
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54 </options>
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55 </param>
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56 </when>
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57
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58 <when value="history">
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59 <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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60 </when>
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61 </conditional>
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62
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63 <conditional name="paired">
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64 <param name="sPaired" type="select" label="Is this library mate-paired?">
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65 <option value="single">Single-end</option>
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66 <option value="paired">Paired-end</option>
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67 </param>
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68
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69 <when value="single">
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70 <param name="input1" type="data" format="fastq" label="FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
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71 </when>
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72 <when value="paired">
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73 <param name="input1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
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74 <param name="input2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
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75 </when>
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76 </conditional>
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77 <conditional name="params">
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78 <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
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79 <option value="preSet">Use Defaults</option>
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80 <option value="full">Full parameter list</option>
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81 </param>
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82 <when value="preSet" />
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83 <!-- Full/advanced parameters. -->
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84 <when value="full">
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85 <!-- Indexing parameters -->
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86 <param name="k" type="text" value="13" label="k-mer length for the index" />
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87 <param name="s" type="text" value="2" label="step size for the index" />
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88 <!-- Alignment Scoring -->
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89 <param name="t" type="text" value="99" label="maximum alignment score" />
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90 <param name="g" type="text" value="40" label="Gap opening penalty" />
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91 <param name="x" type="text" value="6" label="Gap extending penalty" />
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92 <!-- Read preprocessing -->
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93 <param name="n" type="text" value="80" label="Truncate read to specified length" />
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94 <!-- Quality control -->
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95 <param name="l" type="text" value="50" label="minimum number of good quality bases" />
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96 <param name="m" type="text" value="20" label="Repeat filter" />
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97 <param name="H" type="text" value="2" label="Hard clip 3' bases" />
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98 <param name="pairedEnd" type="select" label="Paired End" >
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99 <option value="mp">MP</option>
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100 <option value="pe">PE</option>
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101 <option value="pp">++</option>
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102 <option value="pn">+-</option>
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103 <option value="np">-+</option>
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104 </param>
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105
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106 <param name="i" type="text" value="200" label="Insert size" />
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107 <param name="d" type="text" value="50" label="standard deviation" />
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108
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109 </when> <!-- full -->
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110 </conditional> <!-- params -->
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111
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112
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113 </inputs>
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114 <outputs>
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115 <data format="txt" name="output" label="${tool.name} on ${on_string}:"/>
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116 </outputs>
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117 <help>
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118
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119 **Novoalign**
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120
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121 Novoalign is highly accurate program for mapping next-generation sequencing reads to a reference database. (http://www.novocraft.com/). Selected parameters used here are listed here.
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122
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123 ------
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124
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125 **Indexing usage**
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126
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127 novoindex options indexfile sequencefiles
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128
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129 ------
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130
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131 **Options - Description**
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132
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133 -k 99
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134
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135 kmer length to be used for the index. Novoindex will select appropriate values if either of these is not specified. Default value is log4(N/20s) where N is genome size and s step size.
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136
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137 -s 9
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138
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139 step size for the index. Typical values are from 1 to 3, usually defaults to 1 or 2. Genomes larger than 4Gbp can be indexed using a stepsize > 1, the requirement is N/s less than 4G.
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140
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141 ------
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142
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143 **Alignment usage**
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144
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145 novoalign options
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146
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147 ------
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148
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149 **Options - Description**
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150
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151 -d dbname
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152
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153 Full pathname of indexed reference sequence from novoindex
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154
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155 -f read1 read2
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156
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157 Filenames for the read sequences for Side 1 and 2.
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158
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159 -t 99
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160
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161 Sets absolute threshold or highest alignment score acceptable for the best alignment.
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162
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163 -g 99
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164
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165 Sets the gap opening penalty. Default 40
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166
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167 -x 99
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168
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169 Sets the gap extend penalty. Default 6
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170
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171 -l 99
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172
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173 Sets the minimum number of good quality bases for a read.
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174
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175 -H [99]
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176
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177 Hard clips 3' bases with quality <=[99] from reads before aligning them.
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178
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179
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180
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181 </help>
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182
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183 </tool>
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184
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185
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186
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187
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