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1 <tool id="modencode_peakcalling_ranger" name="PeakRanger" version="1.16">
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2 <description>multi-purpose, ultrafast ChIP Seq peak caller</description>
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3 <command interpreter="python">ranger_wrapper.py $options_file $outputs_file</command>
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4 <requirements>
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5 <requirement type="package">peakranger</requirement>
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6 </requirements>
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7 <inputs>
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8 <param name="experiment_name" type="text" value="PeakRanger in Galaxy" size="50" label="Experiment Name"/>
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9
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10 <conditional name="major_command">
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11 <param name="major_command_selector" type="select" label="Select action to be performed">
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12 <option value="nr">Estimate data quality (nr)</option>
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13 <option value="lc">Calculate library complexity (lc)</option>
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14 <option value="wig">Generate coverage wiggle file (wig)</option>
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15 <option value="wigpe">Generate coverage wiggle file using block models (wigpe)</option>
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16 <option value="ranger">Peak calling for sharp peaks (ranger)</option>
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17 <option value="ccat">Peak calling for broad peaks (ccat)</option>
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18 </param>
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19 <when value="nr">
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20 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
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21 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
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22
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23 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
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24 </when>
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25 <when value="lc">
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26 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
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27 </when>
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28 <when value="wig">
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29 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
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30
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31 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
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32
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33 <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="output will be in .zip format (-s)"/>
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34 <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="output will be in .zip format (-x)"/>
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35 <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
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36 </when>
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37 <when value="wigpe">
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38 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
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39
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40 <param name="extension" type="integer" value="0" label="Read extension length" help="default=0 (-l)"/>
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41
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42 <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="(-s)"/>
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43 <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="(-x)"/>
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44 <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
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45 </when>
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46 <when value="ranger">
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47 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
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48 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
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49
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50 <conditional name="gene_annotate_file">
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51 <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
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52 <option value="dm3refGene.txt">dm3refGene.txt</option>
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53 <option value="hg19refGene.txt">hg19refGene.txt</option>
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54 <option value="mm9refGene.txt">mm9refGene.txt</option>
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55 <option value="Upload">Select from history</option>
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56 <option value="None">None</option>
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57 </param>
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58 <when value="upload">
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59 <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
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60 </when>
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61 </conditional>
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62 <param name="threads" type="integer" value="1" label="Number of threads" help="default=1 (-t)"/>
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63 <param name="plot_region" type="integer" value="6000" label="The length of the snapshot region in the HTML report" help="(--plot_region)"/>
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64 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
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65 <param name="pvalue" type="float" value="0.0001" label="p-value cut-off" help="default=0.0001 (-p)"/>
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66 <param name="fdr" type="float" value="0.01" label="FDR cut-off" help="default=0.01 (-p)"/>
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67 <param name="delta" type="integer" value="1" label="Sensitivity of the summit detector" help="default=1 (-r)"/>
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68 <param name="bandwith" type="integer" value="99" label="Smoothing bandwith" help="default=99 (-b)"/>
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69
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70 <param name="pad" truevalue="--pad" falsevalue="" type="boolean" checked="False" label="Pad read coverage profile to avoid false positive summits" help="(--pad)"/>
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71 </when>
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72 <when value="ccat">
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73 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
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74 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
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75
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76 <conditional name="gene_annotate_file">
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77 <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
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78 <option value="dm3refGene.txt">dm3refGene.txt</option>
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79 <option value="hg19refGene.txt">hg19refGene.txt</option>
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80 <option value="mm9refGene.txt">mm9refGene.txt</option>
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81 <option value="Upload">Select from history</option>
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82 <option value="None">None</option>
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83 </param>
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84 <when value="upload">
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85 <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
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86 </when>
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87 </conditional>
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88 <param name="plot_region" type="integer" value="6000" label="Read extension length" help="default=6000 (--plot_region)"/>
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89 <param name="extension" type="integer" value="100" label="Read extension length" help="default=100 (-l)"/>
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90 <param name="fdr" type="float" value="0.11" label="FDR cut-off" help="default=0.11 (-q)"/>
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91 <param name="winsize" type="integer" value="500" label="Sliding window size" help="default=500 (--win_size)"/>
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92 <param name="winstep" type="integer" value="50" label="Window moving step" help="default=50 (--win_step)"/>
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93 <param name="mincount" type="integer" value="4" label="Minimum window reads count" help="default=4 (--min_count)"/>
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94 <param name="minscore" type="integer" value="5" label="Minimum window reads fold change" help="default=5 (--min_score)"/>
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95 </when>
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96 </conditional>
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97 </inputs>
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98
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99 <outputs>
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100 <data name="output_ranger_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
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101 <filter>major_command['major_command_selector'] == 'nr' or major_command['major_command_selector'] == 'lc' or major_command['major_command_selector'] == 'ccat'</filter>
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102 </data>
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103 <data name="output_wigzip_file" format="wig, zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
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104 <filter>major_command['major_command_selector'] == 'wig' or major_command['major_command_selector'] == 'wigpe'</filter>
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105 </data>
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106 <data name="output_summit_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (summit)">
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107 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
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108 </data>
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109 <data name="output_region_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (region)">
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110 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
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111 </data>
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112 <data name="output_details_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (details)">
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113 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
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114 </data>
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115 <data name="output_report_file" format="zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (html report)">
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116 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
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117 <filter>major_command['gene_annotate_file']['gene_annotate_file_selector'] != 'None'</filter>
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118 </data>
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119 </outputs>
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120
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121 <configfiles>
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122 <configfile name="outputs_file"><%
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123 import simplejson
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124 %>
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125 ##=======================================================================================
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126 #set $__outputs = { 'command':str( $major_command.major_command_selector ) }
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127 #if str( $major_command.major_command_selector ) == 'nr' or str( $major_command.major_command_selector ) == 'lc':
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128 #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
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129 #end if
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130 ##=======================================================================================
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131 #if str( $major_command.major_command_selector ) == 'wig' or str( $major_command.major_command_selector ) == 'wigpe':
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132 #set $__outputs['output_wigzip_file'] = str( $output_wigzip_file )
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133 #end if
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134 ##=======================================================================================
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135 #if str( $major_command.major_command_selector ) == 'ranger' or str( $major_command.major_command_selector ) == 'ccat':
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136 #set $__outputs['output_summit_file'] = str( $output_summit_file )
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137 #set $__outputs['output_region_file'] = str( $output_region_file )
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138 #set $__outputs['output_details_file'] = str( $output_details_file )
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139 #set $__outputs['output_report_file'] = str( $output_report_file )
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140 #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
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141 #end if
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142 ##=======================================================================================
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143 ${ simplejson.dumps( __outputs ) }
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144 </configfile>
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145 <configfile name="options_file"><%
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146 import simplejson
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147 %>
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148 #set $__options = { 'experiment_name':str($experiment_name), 'action':str( $major_command.major_command_selector ) }
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149
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150 ##=============================================================================
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151 #if str($major_command.major_command_selector) == 'nr':
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152 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
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153 #set $__options['input_file'] = str( $major_command.input_control_file1 )
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154
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155 #set $__options['extension'] = str( $major_command.extension )
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156 #end if
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157 ##=============================================================================
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158 ##if str($major_command.major_command_selector) == 'lc':
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159 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
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160 ##end if
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161 ##=============================================================================
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162 #if str($major_command.major_command_selector) == 'wig' or str($major_command.major_command_selector) == 'wigpe':
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163 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
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164
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165 #set $__options['extension'] = str( $major_command.extension )
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166 #set $__options['split'] = str( $major_command.split )
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167 #set $__options['strand'] = str( $major_command.strand)
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168 #set $__options['gzip'] = str( $major_command.gzip )
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169 #end if
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170 ##=============================================================================
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171 #if str($major_command.major_command_selector) == 'ranger':
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172 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
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173 #set $__options['input_file'] = str( $major_command.input_control_file1 )
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174
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175 #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
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176 #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
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177 #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file )
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178 #end if
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179
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180 #set $__options['plot_region'] = str( $major_command.plot_region )
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181 #set $__options['pvalue'] = str( $major_command.pvalue )
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182 #set $__options['fdr'] = str( $major_command.fdr )
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183 #set $__options['extension'] = str( $major_command.extension )
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184 #set $__options['delta'] = str( $major_command.delta )
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185 #set $__options['threads'] = str( $major_command.threads )
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186 #set $__options['bandwith'] = str( $major_command.bandwith )
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187 #set $__options['pad'] = str( $major_command.pad )
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188 #end if
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189 ##=============================================================================
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190 #if str($major_command.major_command_selector) == 'ccat':
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191 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
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192 #set $__options['input_file'] = str( $major_command.input_control_file1 )
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193
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194 #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
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195 #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
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196 #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file )
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197 #end if
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198
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199 #set $__options['plot_region'] = str( $major_command.plot_region )
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200 #set $__options['fdr'] = str( $major_command.fdr )
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201 #set $__options['extension'] = str( $major_command.extension )
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202 #set $__options['winsize'] = str( $major_command.winsize )
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203 #set $__options['winstep'] = str( $major_command.winstep )
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204 #set $__options['mincount'] = str( $major_command.mincount )
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205 #set $__options['minscore'] = str( $major_command.minscore )
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206 #end if
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207 ##=============================================================================
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208 ${ simplejson.dumps( __options ) }
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209 </configfile>
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210 </configfiles>
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211 <tests>
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212 <!--none yet for macs2-->
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213 </tests>
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214 <help>
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215 **What it does**
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216
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217 PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:
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218
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219 View the modified PeakRanger documentation: http://ranger.sourceforge.net/manualv116.html#introduction
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220
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221 ------
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222
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223 **Usage**
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224
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225 **nr:** noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment
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226
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227 **lc:** library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.
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228
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229 **wig:** coverage file generator. Generates variable step format wiggle file
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230
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231 **wigpe:** coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files
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232
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233 wigpe can also generate coverage files for bam files containing spliced reads, such as those from RNA-Seq experiments.
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234
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235 **ranger:** ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.
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236
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237 **ccat:** ChIP-Seq peak caller. Tuned for the discovery of broad peaks
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238
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239 Both ranger and ccat supports generating HTML-based annotation reports.
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240
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241 ------
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242
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243 **Citation**
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244
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245 If you use PeakRanger in your research, please cite:
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246 Feng X, Grossman R, Stein L: PeakRanger:A cloud-enabled peak caller for ChIP-seq data.BMC Bioinformatics 2011, 12(1):139.
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247
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248 if you use the ccat tool, please also cite:
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249 Xu, H., L. Handoko, et al. (2010).A signal-noise model for significance analysis of ChIP-seq with negative control.Bioinformatics 26(9): 1199-1204.
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250
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251
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252 Integration of PeakRanger with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.
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253 </help>
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254 </tool>
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