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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'>
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4 bsmap
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5 </requirement>
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6 </requirements>
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7 <command interpreter="bash">
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8 bsmap_wrapper.sh
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9 ##Reference genome
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10 ##ref="${reference.fields.path}"
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11 #if $refGenomeSource.genomeSource == "history":
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12 ref="${refGenomeSource.myFile.extra_files_path}/${refGenomeSource.myFile.metadata.base_name}"
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13 #else
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14 ref="${refGenomeSource.builtin.fields.path}"
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15 #end if
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16 ##Output files (SAM output, BSMAP summary)
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17 mapped=$mapped
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18 ##Temp directory
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19 tempdir=$mapped.files_path
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20 summary=$summary
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21 #if str($singlePaired.sPaired) == "single":
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22 library="single"
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23 mate1=$singlePaired.sInput1
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24 #if str($singlePaired.sParams.sSettingsType) == "full":
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25 fullparam=true
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26 qual=$singlePaired.sParams.qual
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27 threshold=$singlePaired.sParams.threshold
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28 lowqual=$singlePaired.sParams.lowqual
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29 adapter=$singlePaired.sParams.adapter
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30 firstn=$singlePaired.sParams.firstn
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31 repeat_reads=$singlePaired.sParams.repeat_reads
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32 seed_size=$singlePaired.sParams.seed_size
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33 mismatch=$singlePaired.sParams.mismatch
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34 equal_best=$singlePaired.sParams.equal_best
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35 start=$singlePaired.sParams.start
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36 end=$singlePaired.sParams.end
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37 index_interval=$singlePaired.sParams.index_interval
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38 seed_random=$singlePaired.sParams.seed_random
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39 rrbs=$singlePaired.sParams.rrbs
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40 mode=$singlePaired.sParams.mode
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41 align_info=$singlePaired.sParams.align_info
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42 #end if
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43 #else:
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44 library="paired"
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45 mate1=$singlePaired.pInput1
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46 mate2=$singlePaired.pInput2
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47 unpaired=$unpaired
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48 #if str($singlePaired.pParams.pSettingsType) == "full":
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49 fullparam=true
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50 qual=$singlePaired.pParams.qual
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51 threshold=$singlePaired.pParams.threshold
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52 lowqual=$singlePaired.pParams.lowqual
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53 adapter=$singlePaired.pParams.adapter
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54 firstn=$singlePaired.pParams.firstn
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55 repeat_reads=$singlePaired.pParams.repeat_reads
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56 seed_size=$singlePaired.pParams.seed_size
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57 mismatch=$singlePaired.pParams.mismatch
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58 equal_best=$singlePaired.pParams.equal_best
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59 start=$singlePaired.pParams.start
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60 end=$singlePaired.pParams.end
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61 index_interval=$singlePaired.pParams.index_interval
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62 seed_random=$singlePaired.pParams.seed_random
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63 rrbs=$singlePaired.pParams.rrbs
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64 mode=$singlePaired.pParams.mode
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65 align_info=$singlePaired.pParams.align_info
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66 maxinsert=$singlePaired.pParams.maxinsert
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67 mininsert=$singlePaired.pParams.mininsert
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68 #end if
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69 #end if
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70 </command>
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71 <inputs>
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72
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73 <conditional name="refGenomeSource">
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74 <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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75 <option value="builtin">Use a built-in index</option>
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76 <option value="history">Use one from the history</option>
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77 </param>
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78 <when value="builtin">
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79 <param name="index" type="select" label="Select a reference genome">
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80 <options from_data_table="bsmap_fasta">
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81 <filter type="sort_by" column="2" />
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82 <validator type="no_options" message="No reference genomes are available" />
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83 </options>
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84 </param>
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85 </when>
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86 <when value="history">
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87 <param name="myFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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88 </when>
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89 </conditional>
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90
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91 <conditional name="singlePaired">
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92 <param name="sPaired" type="select" label="Is this library mate-paired?">
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93 <option value="single">Single-end</option>
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94 <option value="paired">Paired-end</option>
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95 </param>
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96 <when value="single">
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97 <param name="sInput1" type="data" format="fastq,fasta" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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98 <conditional name="sParams">
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99 <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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100 <option value="preSet">Commonly used</option>
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101 <option value="full">Full parameter list</option>
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102 </param>
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103 <when value="preSet" />
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104 <when value="full">
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105 <param name="qual" type="select" label="Select the type of FastQ qualities">
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106 <option value="33">phred33-quals</option>
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107 <option value="64">phred64-quals</option>
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108 </param>
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109 <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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110 <param name="lowqual" type="integer" value="5" label="Filter low-quality reads containing >n Ns" help="default=5" />
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111 <param name="adapter" type="text" value="none" label="3-end adapter sequence" help="default: none (no trim)" />
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112 <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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113
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114 <param name="repeat_reads" type="select" label="How to report repeat hits">
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115 <option value="0">none(unique hit only)</option>
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116 <option value="1">random one</option>
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117 </param>
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118
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119 <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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120 <param name="mismatch" type="integer" value="2" label="Maximum number of mismatches allowed on a read" max="15" />
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121 <param name="equal_best" type="integer" value="20" label="Maximum number of equal best hits to count" max="1000" />
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122 <param name="start" type="integer" value="1" label="Start from the Nth read or read pair" />
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123 <param name="end" type="integer" value="4294967295" label="End at the Nth read or read pair" />
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124 <param name="index_interval" type="integer" value="4" label="Index interval" />
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125 <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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126 <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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127 <param name="mode" type="select" label="Set mapping strand information">
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128 <option value="0">only map to 2 forward strands</option>
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129 <option value="1">map SE or PE reads to all 4 strands</option>
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130 </param>
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131 <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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132 </when> <!-- full -->
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133 </conditional> <!-- sParams -->
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134 </when> <!-- single -->
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135
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136 <when value="paired">
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137 <param name="pInput1" type="data" format="fastq,fasta" label="Forward FASTQ file" />
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138 <param name="pInput2" type="data" format="fastq,fasta" label="Reverse FASTQ file" />
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139
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140 <conditional name="pParams">
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141 <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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142 <option value="preSet">Commonly used</option>
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143 <option value="full">Full parameter list</option>
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144 </param>
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145 <when value="preSet" />
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146 <when value="full">
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147 <param name="qual" type="select" label="Select the type of FastQ qualities">
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148 <option value="33">phred33-quals</option>
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149 <option value="64">phred64-quals</option>
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150 </param>
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151
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152 <param name="mininsert" type="integer" value="28" label="Minimal insert size allowed" />
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153 <param name="maxinsert" type="integer" value="500" label="Maximal insert size allowed" />
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154
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155 <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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156 <param name="lowqual" type="integer" value="5" label="Filter low-quality reads containing >n Ns" help="default=5" />
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157 <param name="adapter" type="text" value="none" label="3-end adapter sequence" help="default: none (no trim)" />
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158 <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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159
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160 <param name="repeat_reads" type="select" label="How to report repeat hits">
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161 <option value="0">none(unique hit only)</option>
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162 <option value="1">random one</option>
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163 </param>
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164
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165 <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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166 <param name="mismatch" type="integer" value="2" label="Maximum number of mismatches allowed on a read" max="15" />
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167 <param name="equal_best" type="integer" value="20" label="Maximum number of equal best hits to count" max="1000" />
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168 <param name="start" type="integer" value="1" label="Start from the Nth read or read pair" />
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169 <param name="end" type="integer" value="4294967295" label="End at the Nth read or read pair" />
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170 <param name="index_interval" type="integer" value="4" label="Index interval" />
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171 <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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172 <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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173 <param name="mode" type="select" label="Set mapping strand information">
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174 <option value="0">only map to 2 forward strands</option>
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175 <option value="1">map SE or PE reads to all 4 strands</option>
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176 </param>
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177 <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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178
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179
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180 </when> <!-- full -->
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181 </conditional> <!-- pParams -->
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182 </when> <!-- paired -->
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183 </conditional> <!-- singlePaired -->
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184
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185
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186 </inputs>
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187 <outputs>
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188 <data name="mapped" format="sam" label="BSMAP Mapped Reads">
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189 <actions>
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190 <action type="metadata" name="dbkey">
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191 <option type="from_data_table" name="bsmap_fasta" column="1" offset="0">
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192 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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193 <filter type="param_value" ref="reference" column="0"/>
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194 </option>
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195 </action>
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196 </actions>
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197 </data>
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198 <data name="summary" format="txt" label="BSMAP Mapping Summary" />
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199 <data name="unpaired" format ="sam" label="BSMAP Unpaired Hits">
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200 <filter>(singlePaired['sPaired'] == 'paired')</filter>
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201 </data>
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202
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203 </outputs>
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204 <help>
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205 **What it does**
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206
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207 BSMAP is a short reads mapping software for bisulfite sequencing reads. It has the following features:
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208
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209 - read length up to 144 nt, allow up to 15 mismatches, gap size up to 3 bp.
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210
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211 - support single end and pair end mapping. support multi-thread mapping.
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212
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213 - support both "Lister protocol" (sequence 2 forward strands only) and "Cokus protocol" (sequence all 4 bisulfite converted strands)
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214
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215 - 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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216
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217 - 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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218
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219 - allow trimming adapter sequences and low quality nucleotides from the 3'end of reads
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220
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221 - 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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222
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223 - 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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224
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225 .. _BSMAP: http://code.google.com/p/bsmap/
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226
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227 **Input formats**
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228
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229 BSMAP accepts files in FASTA/FASTQ format.
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230
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231 **Outputs**
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232
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233 The output contains the following files:
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234
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235 - mapped reads in SAM format
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236
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237 - mapping summary
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238
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239 - unpaired hits (only for paired-end mapping)
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240
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241 </help>
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242
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243 <tests>
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244 </tests>
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245 </tool>
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246
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