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1 <tool id="bsmap" name="BSMAP Mapper">
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2 <requirements>
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3 <requirement type='package' version="2.6">bsmap</requirement>
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4 </requirements>
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5 <command interpreter="bash">
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6 bsmap_wrapper.sh
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7 ##Reference genome
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8 ##ref="${reference.fields.path}"
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9 #if $refGenomeSource.genomeSource == "history":
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10 ref="${refGenomeSource.myFile}"
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11 #else
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12 ref="${refGenomeSource.builtinFile.fields.path}"
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13 #end if
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14 ##Output files (SAM output, BSMAP summary)
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15 mapped=$mapped
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16 ##Temp directory
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17 tempdir=$mapped.files_path
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18 summary=$summary
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19 #if str($singlePaired.sPaired) == "single":
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20 library="single"
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21 mate1=$singlePaired.sInput1
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22 #if str($singlePaired.sParams.sSettingsType) == "full":
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23 fullparam=true
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24 qual=$singlePaired.sParams.qual
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25 threshold=$singlePaired.sParams.threshold
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26 lowqual=$singlePaired.sParams.lowqual
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27 adapter=$singlePaired.sParams.adapter
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28 firstn=$singlePaired.sParams.firstn
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29 repeat_reads=$singlePaired.sParams.repeat_reads
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30 seed_size=$singlePaired.sParams.seed_size
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31 mismatch=$singlePaired.sParams.mismatch
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32 equal_best=$singlePaired.sParams.equal_best
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33 start=$singlePaired.sParams.start
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34 end=$singlePaired.sParams.end
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35 index_interval=$singlePaired.sParams.index_interval
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36 seed_random=$singlePaired.sParams.seed_random
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37 rrbs=$singlePaired.sParams.rrbs
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38 mode=$singlePaired.sParams.mode
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39 align_info=$singlePaired.sParams.align_info
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40 #end if
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41 #else:
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42 library="paired"
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43 mate1=$singlePaired.pInput1
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44 mate2=$singlePaired.pInput2
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45 unpaired=$unpaired
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46 #if str($singlePaired.pParams.pSettingsType) == "full":
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47 fullparam=true
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48 qual=$singlePaired.pParams.qual
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49 threshold=$singlePaired.pParams.threshold
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50 lowqual=$singlePaired.pParams.lowqual
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51 adapter=$singlePaired.pParams.adapter
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52 firstn=$singlePaired.pParams.firstn
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53 repeat_reads=$singlePaired.pParams.repeat_reads
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54 seed_size=$singlePaired.pParams.seed_size
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55 mismatch=$singlePaired.pParams.mismatch
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56 equal_best=$singlePaired.pParams.equal_best
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57 start=$singlePaired.pParams.start
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58 end=$singlePaired.pParams.end
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59 index_interval=$singlePaired.pParams.index_interval
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60 seed_random=$singlePaired.pParams.seed_random
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61 rrbs=$singlePaired.pParams.rrbs
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62 mode=$singlePaired.pParams.mode
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63 align_info=$singlePaired.pParams.align_info
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64 maxinsert=$singlePaired.pParams.maxinsert
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65 mininsert=$singlePaired.pParams.mininsert
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66 #end if
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67 #end if
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68 </command>
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69 <inputs>
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70
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71 <conditional name="refGenomeSource">
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72 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
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73 <option value="builtin">Use a built-in reference</option>
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74 <option value="history">Use one from the history</option>
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75 </param>
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76 <when value="builtin">
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77 <param name="builtinFile" type="select" label="Select the reference genome">
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78 <options from_data_table="bsmap_fasta">
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79 <filter type="sort_by" column="2" />
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80 <validator type="no_options" message="No reference genomes are available" />
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81 </options>
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82 </param>
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83 </when>
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84 <when value="history">
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85 <param name="myFile" type="data" format="fasta" label="Select the reference genome" />
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86 </when>
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87 </conditional>
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88
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89 <conditional name="singlePaired">
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90 <param name="sPaired" type="select" label="Is this library mate-paired?">
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91 <option value="single">Single-end</option>
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92 <option value="paired">Paired-end</option>
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93 </param>
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94 <when value="single">
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95 <param name="sInput1" type="data" format="fastq,fasta" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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96 <conditional name="sParams">
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97 <param name="sSettingsType" type="select" label="BSMAP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
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98 <option value="preSet">Commonly used</option>
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99 <option value="full">Full parameter list</option>
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100 </param>
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101 <when value="preSet" />
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102 <when value="full">
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103 <param name="qual" type="select" label="Select the type of FastQ qualities">
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104 <option value="33">phred33-quals</option>
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105 <option value="64">phred64-quals</option>
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106 </param>
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107 <param name="threshold" type="integer" value="0" label="Quality threshold in trimming" help="0-40, default=0 (no trim)" min="0" max="40" />
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108 <param name="lowqual" type="integer" value="5" label="Filter low-quality reads containing >n Ns" help="default=5" />
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109 <param name="adapter" type="text" value="none" label="3-end adapter sequence" help="default: none (no trim)" />
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110 <param name="firstn" type="integer" value="144" label="Map the first N nucleotides of the read" help="default:144 (map the whole read)" />
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111
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112 <param name="repeat_reads" type="select" label="How to report repeat hits">
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113 <option value="0">none(unique hit only)</option>
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114 <option value="1">random one</option>
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115 </param>
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116
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117 <param name="seed_size" type="integer" value="16" label="Seed size" min="8" max="16" help="default=16(WGBS mode), 12(RRBS mode)" />
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118 <param name="mismatch" type="integer" value="2" label="Maximum number of mismatches allowed on a read" max="15" />
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119 <param name="equal_best" type="integer" value="20" label="Maximum number of equal best hits to count" max="1000" />
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120 <param name="start" type="integer" value="1" label="Start from the Nth read or read pair" />
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121 <param name="end" type="integer" value="4294967295" label="End at the Nth read or read pair" />
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122 <param name="index_interval" type="integer" value="4" label="Index interval" />
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123 <param name="seed_random" type="integer" value="-1" label="Seed for random number generation used in selecting multiple hits" help="other seed values generate pseudo random number based on read index number, to allow reproducible mapping results" />
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124 <param name="rrbs" type="text" value="none" label="Activating RRBS mapping mode and set restriction enzyme digestion sites" help="digestion position marked by '-', example: -D C-CGG for MspI digestion. default: none (whole genome shotgun bisulfite mapping mode)" />
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125 <param name="mode" type="select" label="Set mapping strand information">
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126 <option value="0">only map to 2 forward strands</option>
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127 <option value="1">map SE or PE reads to all 4 strands</option>
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128 </param>
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129 <param name="align_info" type="text" value="none" label="Set alignment information for the additional nucleotide transition" help="is in the form of two different nucleotides N1N2,indicating N1 in the reads could be mapped to N2 in the reference sequences. default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. example: -M GA could be used to detect A=>I(G) transition in RNA editing." />
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130 </when> <!-- full -->
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131 </conditional> <!-- sParams -->
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132 </when> <!-- single -->
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133
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134 <when value="paired">
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135 <param name="pInput1" type="data" format="fastq,fasta" label="Forward FASTQ file" />
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136 <param name="pInput2" type="data" format="fastq,fasta" label="Reverse FASTQ file" />
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137
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138 <conditional name="pParams">
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139 <param name="pSettingsType" type="select" label="BSMAP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
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140 <option value="preSet">Commonly used</option>
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141 <option value="full">Full parameter list</option>
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142 </param>
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143 <when value="preSet" />
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144 <when value="full">
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145 <param name="qual" type="select" label="Select the type of FastQ qualities">
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146 <option value="33">phred33-quals</option>
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147 <option value="64">phred64-quals</option>
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148 </param>
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149
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150 <param name="mininsert" type="integer" value="28" label="Minimal insert size allowed" />
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151 <param name="maxinsert" type="integer" value="500" label="Maximal insert size allowed" />
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152
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153 <param name="threshold" type="integer" value="0" label="Quality threshold in trimming" help="0-40, default=0 (no trim)" min="0" max="40" />
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154 <param name="lowqual" type="integer" value="5" label="Filter low-quality reads containing >n Ns" help="default=5" />
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155 <param name="adapter" type="text" value="none" label="3-end adapter sequence" help="default: none (no trim)" />
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156 <param name="firstn" type="integer" value="144" label="Map the first N nucleotides of the read" help="default:144 (map the whole read)" />
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157
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158 <param name="repeat_reads" type="select" label="How to report repeat hits">
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159 <option value="0">none(unique hit only)</option>
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160 <option value="1">random one</option>
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161 </param>
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162
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163 <param name="seed_size" type="integer" value="16" label="Seed size" min="8" max="16" help="default=16(WGBS mode), 12(RRBS mode)" />
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164 <param name="mismatch" type="integer" value="2" label="Maximum number of mismatches allowed on a read" max="15" />
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165 <param name="equal_best" type="integer" value="20" label="Maximum number of equal best hits to count" max="1000" />
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166 <param name="start" type="integer" value="1" label="Start from the Nth read or read pair" />
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167 <param name="end" type="integer" value="4294967295" label="End at the Nth read or read pair" />
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168 <param name="index_interval" type="integer" value="4" label="Index interval" />
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169 <param name="seed_random" type="integer" value="-1" label="Seed for random number generation used in selecting multiple hits" help="other seed values generate pseudo random number based on read index number, to allow reproducible mapping results" />
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170 <param name="rrbs" type="text" value="none" label="Activating RRBS mapping mode and set restriction enzyme digestion sites" help="digestion position marked by '-', example: -D C-CGG for MspI digestion. default: none (whole genome shotgun bisulfite mapping mode)" />
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171 <param name="mode" type="select" label="Set mapping strand information">
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172 <option value="0">only map to 2 forward strands</option>
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173 <option value="1">map SE or PE reads to all 4 strands</option>
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174 </param>
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175 <param name="align_info" type="text" value="none" label="Set alignment information for the additional nucleotide transition" help="is in the form of two different nucleotides N1N2,indicating N1 in the reads could be mapped to N2 in the reference sequences. default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. example: -M GA could be used to detect A=>I(G) transition in RNA editing." />
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176
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177
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178 </when> <!-- full -->
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179 </conditional> <!-- pParams -->
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180 </when> <!-- paired -->
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181 </conditional> <!-- singlePaired -->
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182
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183
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184 </inputs>
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185 <outputs>
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186 <data name="mapped" format="sam" label="BSMAP Mapped Reads" />
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187 <data name="summary" format="txt" label="BSMAP Mapping Summary" />
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188 <data name="unpaired" format ="sam" label="BSMAP Unpaired Hits">
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189 <filter>(singlePaired['sPaired'] == 'paired')</filter>
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190 </data>
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191
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192 </outputs>
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193 <help>
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194 **What it does**
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195
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196 BSMAP is a short reads mapping software for bisulfite sequencing reads. It has the following features:
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197
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198 - read length up to 144 nt, allow up to 15 mismatches, gap size up to 3 bp.
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199
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200 - support single end and pair end mapping. support multi-thread mapping.
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201
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202 - support both "Lister protocol" (sequence 2 forward strands only) and "Cokus protocol" (sequence all 4 bisulfite converted strands)
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203
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204 - reads are directly mapped to original reference genome sequence, no need to preprocess the reads and reference genome to convert C to T.
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205
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206 - support both whole genome bisulfite sequencing (WGBS) mode and reduced representation bisulfite sequencing (RRBS) mode, allow changing the digestion site information to support different digestion enzymes for RRBS.
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207
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208 - allow trimming adapter sequences and low quality nucleotides from the 3'end of reads
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209
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210 - allow trade off between speed/memory usage/mapping sensitivity. For human genome, the RRBS mode uses ~3GB. In WGBS mode, the typical memory usage is ~9GB, but can be as low as 5GB.
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211
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212 - allow alignment for other nucleotide transitions, for example, can be set to detect the A=>I(G) transition in RNA editing.
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213
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214 .. _BSMAP: http://code.google.com/p/bsmap/
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215
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216 **Input formats**
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217
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218 BSMAP accepts files in FASTA/FASTQ format.
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219
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220 **Outputs**
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221
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222 The output contains the following files:
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223
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224 - mapped reads in SAM format
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225
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226 - mapping summary
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227
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228 - unpaired hits (only for paired-end mapping)
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229
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230 </help>
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231
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232 <tests>
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233 </tests>
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234 </tool>
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235
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