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1 <tool id="methyation_extractor_tool" name="Methylation Extractor" version="0.7.6">
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2 <description>: extracts the methylation information for individual cytosine</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.16">samtools</requirement>
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5 <requirement type="package" version="0.12.7">bowtie2</requirement>
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6 <requirement type="package" version="0.7.6">bismark</requirement>
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7 </requirements>
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8 <command interpreter="perl">
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9
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10 methylation_extractor_wrapper.pl
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11
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12
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13 "GENOME::${genome.fields.path}"
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14
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15
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16 #if str($no_overlap) == "ON":
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17 "OPTION::--no_overlap"
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18 #end if
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19
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20 #if str($ending) == "single":
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21 "ENDING::-s"
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22 #else
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23 "ENDING::-p"
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24 #end if
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25
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26 #if str($report) == "ON":
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27 "OPTION::--report"
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28 #end if
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29
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30 "OPTION::--bedGraph"
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31
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32 "OPTION::--counts"
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33
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34
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35 "OUTPUT::$output"
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36 "SUMMARY::$summary"
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37
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38 "BAMFILE::$bamfile"
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39
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40
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41 </command>
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42 <inputs>
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43
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44 <param name="genome" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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45 <options from_data_table="bismark_indexes">
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46 <filter type="sort_by" column="2"/>
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47 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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48 </options>
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49 </param>
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50
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51 <param name="bamfile" type="data" format="bam" label="Bam file: bismark output" />
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52
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53 <param name="ending" type="select" label="ending" help="" optional="true">
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54 <option value="single" >single-end</option>
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55 <option value="paired" selected="true">paired-end</option>
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56 </param>
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57
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58 <param name="no_overlap" type="select" label="no-overlap" help="" optional="true">
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59 <option value="ON" selected="true">ON</option>
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60 <option value="OFF">OFF</option>
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61 </param>
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62
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63 <param name="report" type="select" label="Report" help="" optional="true">
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64 <option value="ON" selected="true">ON</option>
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65 <option value="OFF">OFF</option>
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66 </param>
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67
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68 </inputs>
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69 <outputs>
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70 <data format="bedgraph" name="output" label="${tool.name} on ${on_string}">
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71 <actions>
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72 <action type="metadata" name="dbkey">
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73 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
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74 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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75 <filter type="param_value" ref="genome" column="0"/>
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76 </option>
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77 </action>
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78 </actions>
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79 </data>
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80 <data name="summary" format="txt" label="${tool.name} summary" />
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81 </outputs>
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82 <help>
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83 |
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84
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85 **Reference**
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86
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87 http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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88
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89 -----
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90
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91 **What it does**
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92
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93
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94
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95 The script reads in a bisulfite read alignment results file
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96 produced by the Bismark bisulfite mapper (BAM file) and extracts the methylation
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97 informationfor individual cytosines. This information is found in the methylation
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98 call field which can contain the following characters:
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99
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100 ::
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101
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102 ~~~ X for methylated C in CHG context (was protected) ~~~
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103
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104 ~~~ x for not methylated C CHG (was converted) ~~~
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105
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106 ~~~ H for methylated C in CHH context (was protected) ~~~
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107
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108 ~~~ h for not methylated C in CHH context (was converted) ~~~
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109
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110 ~~~ Z for methylated C in CpG context (was protected) ~~~
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111
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112 ~~~ z for not methylated C in CpG context (was converted) ~~~
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113
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114 ~~~ . for any bases not involving cytosines ~~~
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115
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116
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117
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118 -----
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119
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120 **Required Parameters**
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121
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122 ::
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123
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124 -s/--single-end Input file(s) are Bismark result file(s) generated from single-end
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125 read data. Specifying either --single-end or --paired-end is
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126 mandatory.
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127
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128 -p/--paired-end Input file(s) are Bismark result file(s) generated from paired-end
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129 read data. Specifying either --paired-end or --single-end is
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130 mandatory.
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131
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132 --no_overlap For paired-end reads it is theoretically possible that read_1 and
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133 read_2 overlap. This option avoids scoring overlapping methylation
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134 calls twice (only methylation calls of read 1 are used for in the process
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135 since read 1 has historically higher quality basecalls than read 2).
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136 Whilst this option removes a bias towards more methylation calls
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137 in the center of sequenced fragments it may de facto remove a sizable
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138 proportion of the data. This option is highly recommended for paired-end
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139 data.
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140
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141 --report Prints out a short methylation summary as well as the paramaters used to run
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142 this script.
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143
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144
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145 -----
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146
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147 **Default Parameters**
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148
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149 ::
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150
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151 --bedGraph After finishing the methylation extraction, the methylation output is written into a
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152 sorted bedGraph file that reports the position of a given cytosine and its methylation
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153 state (in %, seem details below). The methylation extractor output is temporarily split up into
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154 temporary files, one per chromosome (written into the current directory or folder
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155 specified with -o/--output); these temp files are then used for sorting and deleted
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156 afterwards. By default, only cytosines in CpG context will be sorted. The option
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157 '--CX_context' may be used to report all cyosines irrespective of sequence context
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158 (this will take MUCH longer!).
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159
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160
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161
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162 </help>
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163 </tool>
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164
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165
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