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1 <tool id="bs_seeker_wrapper" name="BS-Seeker2" version="2.0.0">
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2 <requirements><requirement type='package'>bs_seeker2</requirement></requirements>
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3 <description>Versatile aligner for bisulfite sequencing data</description>
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4 <command interpreter="python">
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5 bs_seeker2_wrapper.py
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6 ### define exec path
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7 ### --exec-path "/u/home/galaxy/galaxy/GalaxyTools/bin"
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8 ### [Please change the following path to your local directory]
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9 --exec-path "/Users/weilong/Documents/program/BSseeker2"
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10 ### output
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11 --align--output $align_output
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12 --call_methylation--wig $call_methylation_wig
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13 --call_methylation--CGmap $call_methylation_CGmap
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14 --call_methylation--ATCGmap $call_methylation_ATCGmap
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15 --call_methylation--txt
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16
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17 #if $singlePaired.sPaired == "paired"
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18 --align--input_1 $input1
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19 --align--input_2 $singlePaired.input2
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20 #end if
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21
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22
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23 ### aligner
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24 --align--aligner ${choosealigner.aligner}
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25 #if $choosealigner.aligner == "bowtie2"
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26 #if $choosealigner.mode_type == "local"
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27 --align--bt2--local
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28 #else
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29 --align--bt2--end-to-end
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30 #end if
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31 #end if
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32
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33 ### Index from history or built-in
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34 #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"
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35 --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
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36 --build--aligner ${choosealigner.aligner}
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37 --align-g ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
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38 --align--db ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
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39 #else if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "indexed"
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40 --align--db ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}
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41 --align-g ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}/${choosealigner.rrbsFragments.refGenomeSource.index.fields.dbkey}.fa
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42
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43 #end if
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44
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45 ### RRBS or WGBS
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46 #if $choosealigner.rrbsFragments.Fragmented == "Yes"
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47 #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"
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48 --build--rrbs
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49 --build--low ${choosealigner.rrbsFragments.lowerBound}
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50 --build--up ${choosealigner.rrbsFragments.upperBound}
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51 #end if
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52 --align--rrbs
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53 --align--low ${choosealigner.rrbsFragments.lowerBound}
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54 --align--up ${choosealigner.rrbsFragments.upperBound}
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55 #end if
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56
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57
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58
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59 ### Inputs
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60 #if $singlePaired.sPaired == "single"
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61 --align-i $input1
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62 #end if
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63
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64 ### Library type
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65 --align-t $tag
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66
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67 ### other general options
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68 #if $sParams.sSettingsType == "preSet"
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69 --align--start_base 1
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70 --align--end_base 200
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71 --align--mis 4
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72 #end if
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73
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74 ### adapter information
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75 #if $adapterInfo.useAdapter == "Yes"
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76 --align--adapter ${adapterInfo.adapter_file}
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77 #end if
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78
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79 #if $sParams.sSettingsType == "full"
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80 --align--start_base ${sParams.start_base}
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81 --align--end_base ${sParams.end_base}
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82 --align--mis ${sParams.num_mismatch}
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83 #end if
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84
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85 </command>
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86 <inputs>
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87 <param format="fastq,fasta,qseq" name="input1" type="data" label="Input your read file" help="reads file in fastq, qseq or fasta format" />
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88 <conditional name="singlePaired">
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89 <param name="sPaired" type="select" label="Is this library mate-paired?">
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90 <option value="single">Single-end</option>
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91 <option value="paired">Paired-end</option>
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92 </param>
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93 <when value="paired">
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94 <param format="fastq,fasta,qseq" name="input2" type="data" label="Input your read file 2" help="reads in fastq, qseq or fasta format" />
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95 <param name="min_ins_distance" type="integer" value="-1" label=" Minimum insert size for valid paired-end alignments" />
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96 <param name="max_ins_distance" type="integer" value="400" label="Maximum insert size for valid paired-end alignments" />
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97 </when>
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98 </conditional>
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99 <param name="tag" type="select" label="Type of libraries">
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100 <option value="N">directional libraries</option>
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101 <option value="Y">undirectional libraries</option>
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102 </param>
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103 <conditional name="choosealigner">
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104 <param name="aligner" type="select" label="Short reads aligner">
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105 <option value="bowtie">bowtie</option>
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106 <option value="bowtie2">bowtie2</option>
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107 </param>
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108 <when value="bowtie">
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109 <conditional name="rrbsFragments">
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110 <param name="Fragmented" type="select" label="RRBS-seq reads" help="">
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111 <option value="No">No</option>
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112 <option value="Yes">Yes</option>
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113 </param>
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114 <when value="Yes">
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115 <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" />
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116 <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" />
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117 <conditional name="refGenomeSource">
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118 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
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119 <option value="indexed">Use a built-in index</option>
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120 <option value="history">Use one from the history</option>
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121 </param>
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122 <when value="indexed">
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123 <param name="index" type="select" label="Select a reference genome (RRBS, bowtie)">
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124 <options from_data_table="bs_seeker2_indexes_RRBS_bowtie">
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125 <filter type="sort_by" column="2"/>
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126 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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127 </options>
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128 </param>
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129 </when>
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130 <when value="history">
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131 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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132 </when>
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133 </conditional>
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134 </when>
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135 <when value="No">
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136 <conditional name="refGenomeSource">
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137 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
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138 <option value="indexed">Use a built-in index</option>
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139 <option value="history">Use one from the history</option>
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140 </param>
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141 <when value="indexed">
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142 <param name="index" type="select" label="Select a reference genome (WGBS, bowtie)">
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143 <options from_data_table="bs_seeker2_indexes_WGBS_bowtie">
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144 <filter type="sort_by" column="2"/>
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145 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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146 </options>
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147 </param>
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148 </when>
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149 <when value="history">
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150 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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151 </when>
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152 </conditional>
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153 </when>
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154 </conditional>
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155 </when>
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156
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157 <when value="bowtie2">
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158 <conditional name="rrbsFragments">
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159 <param name="Fragmented" type="select" label="RRBS-seq reads" help="">
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160 <option value="No">No</option>
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161 <option value="Yes">Yes</option>
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162 </param>
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163 <when value="Yes">
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164 <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" />
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165 <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" />
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166 <conditional name="refGenomeSource">
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167 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
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168 <option value="indexed">Use a built-in index</option>
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169 <option value="history">Use one from the history</option>
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170 </param>
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171 <when value="indexed">
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172 <param name="index" type="select" label="Select a reference genome (RRBS, bowtie2)">
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173 <options from_data_table="bs_seeker2_indexes_RRBS_bowtie2">
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174 <filter type="sort_by" column="2"/>
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175 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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176 </options>
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177 </param>
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178 </when>
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179 <when value="history">
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180 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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181 </when>
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182 </conditional>
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183 </when>
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184 <when value="No">
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185 <conditional name="refGenomeSource">
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186 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
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187 <option value="indexed">Use a built-in index</option>
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188 <option value="history">Use one from the history</option>
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189 </param>
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190 <when value="indexed">
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191 <param name="index" type="select" label="Select a reference genome (WGBS, bowtie2)">
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192 <options from_data_table="bs_seeker2_indexes_WGBS_bowtie2">
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193 <filter type="sort_by" column="2"/>
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194 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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195 </options>
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196 </param>
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197 </when>
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198 <when value="history">
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199 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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200 </when>
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201 </conditional>
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202 </when>
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203 </conditional>
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204
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205
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206 <conditional name="mode_type">
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207 <param name="mode" type="select" label="Select the mode of Bowtie2">
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208 <option value="local" selected="true"> local alignment </option>
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209 <option value="end_to_end" > end-to-end alignment </option>
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210 </param>
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211 </conditional>
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212 </when>
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213 </conditional>
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214 <conditional name="adapterInfo">
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215 <param name="useAdapter" type="select" label="adapter sequence">
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216 <option value="noAdapter">No</option>
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217 <option value="withAdapter">Yes</option>
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218 </param>
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219 <when value="withAdapter">
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220 <param format="txt" name="adapter_file" type="data" label="Input file of your adaptor sequences" help="Input text file of your adaptor sequences" />
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221 </when>
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222 </conditional>
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223
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224 <conditional name="sParams">
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225 <param name="sSettingsType" type="select" label="BS Seeker2 settings to use" help="You can use the default settings or set customer values for the BS Seeker2 parameters.">
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226 <option value="preSet">User Defaults</option>
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227 <option value="full">Full parameter list</option>
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228 </param>
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229 <when value="preSet" />
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230 <when value="full">
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231 <param name="start_base" type="integer" value="1" label="The start base of the read to be mapped" help="" />
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232 <param name="end_base" type="integer" value="200" label="The end base of the read to be mapped" help="" />
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233
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234 <param name="num_mismatch" type="integer" value="4" label="Number of mismatches" help="(INT) Default: 4" />
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235 </when>
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236 </conditional>
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237
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238 </inputs>
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239
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240 <outputs>
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241 <data format="bam" name="align_output" label="BAM Alignments"> </data>
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242 <data format="wig" name="call_methylation_wig" label="Methylation Levels"> </data>
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243 <data format="tabular" name="call_methylation_CGmap" label="CGmap file"> </data>
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244 <data format="tabular" name="call_methylation_ATCGmap" label="ATCGmap file"> </data>
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245
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246 </outputs>
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247 <help>
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248 **What it does**
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249
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250 BS-Seeker2 is a seamlessly pipeline for mapping bisulfite sequencing data and generating detailed DNA methylome. BS-Seeker2 improves mappability by using local alignment, and is tailored for RRBS library by building special index, with higher efficiency and accuracy. This is the Galaxy version of BS-Seeker2.
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251
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252 ------
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253
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254 **Resources**
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255
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256 The homepage for BS-Seeker2 is http://pellegrini.mcdb.ucla.edu/BS_Seeker2/.
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257
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258 For more information of BS-Seeker2, please refer to https://github.com/BSSeeker/BSseeker2.
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259
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260 ------
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261
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262 **Example**
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263
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264 - Adapter file::
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265
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266 AGATCGGAAGAGCACACGTC
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267
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268
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269 </help>
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270 </tool>
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