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1 <tool id="modencode_peakcalling_spp" name="SPP" version="1.10.1">
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2 <description>SPP cross-correlation analysis package</description>
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3 <command interpreter="python">spp_wrapper.py $options_file $output_narrow_peak $output_region_peak $output_peakshift_file $output_rdata_file $output_plot_file $output_default_file</command>
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4 <inputs>
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5 <!--experiment name and inputs-->
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6 <param name="experiment_name" type="text" value="SPP in Galaxy" size="50" label="Experiment Name"/>
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7
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8 <!--select function to perform-->
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9 <conditional name="major_command">
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10 <param name="major_command_selector" type="select" label="Select action to be performed">
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11 <option value="cross_correlation">Determine strand cross-correlation peak</option>
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12 <option value="peak_calling">Peak calling</option>
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13 <option value="idr">IDR analysis</option>
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14 <option value="custom">Custom settings</option>
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15 </param>
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16 <when value="cross_correlation">
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17 <!--cross correlation options-->
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18 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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19 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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20
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21 <param name="replace" truevalue="-rf" falsevalue="" type="boolean" checked="True" label="Replace existing plot, Rdata, or narrowpeak file (execution aborts if file exists and option not enabled)" help="(-rf)"/>
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22
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23 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
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24 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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25 </when>
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26 <when value="peak_calling">
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27 <!--peak calling options-->
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28 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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29 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
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30
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31 <param name="fdr" type="text" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
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32 <param name="num_peaks" type="text" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
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33 <param name="replace" truevalue="-rf" falsevalue="" type="boolean" checked="True" label="Replace existing plot, Rdata, or narrowpeak file (execution aborts if file exists and option not enabled)" help="(-rf)"/>
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34
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35 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file " help="(-savr)"/>
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36 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="True" label="Save Rdata file" help="(-savd)"/>
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37 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="True" label="Save narrowpeak file" help="(-savn)"/>
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38 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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39 </when>
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40 <when value="idr">
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41 <!--idr options-->
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42 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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43 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
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44
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45 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="300000" help="default=300000 (-npeak)"/>
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46 <param name="replace" truevalue="-rf" falsevalue="" type="boolean" checked="True" label="Replace existing plot, Rdata, or narrowpeak file (execution aborts if file exists and option not enabled)" help="(-rf)"/>
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47
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48 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file" help="(-savr)"/>
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49 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
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50 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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51 </when>
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52 <when value="custom">
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53 <!--custom settings, includes all relevant options here-->
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54 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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55 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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56
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57 <param name="strand_shift" type="text" label="Strand shifts at which cross-correlation is evaluated" size="30" value="-100:5:600" help="default=-100:5:600 (-s)"/>
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58 <param name="excluded_strand_shift" type="text" label="Strand shifts to exclude" value="10:10" help="default=10:(readlen+10) (-x)"/>
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59 <param name="user_defined_strpeak" type="text" label="User defined cross-correlation peak strand shift" help="(-speak)"/>
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60 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
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61 <param name="fdr" type="integer" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
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62 <param name="filter_char" type="text" label="Pattern to use to remove tags that map to specific chromosomes" help="(-filtchr)"/>
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63 <param name="replace" truevalue="-rf" falsevalue="" type="boolean" checked="False" label="Replace existing plot, Rdata, or narrowpeak file (execution aborts if file exists and option not enabled)" help="(-rf)"/>
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64
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65 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="False" label="Save regionpeak file" help="(-savr)"/>
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66 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="False" label="Save peakshift file" help="(-out)"/>
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67 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="False" label="Save Rdata file" help="(-savd)"/>
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68 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="False" label="Save narrowpeak file" help="(-savn)"/>
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69 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="False" label="Save plot file" help="(-savp)"/>
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70 </when>
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71 </conditional>
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72 </inputs>
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73
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74 <outputs>
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75 <data name="output_default_file" format="txt" label="${tool.name} on ${on_string}"/>
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76 <data name="output_narrow_peak" format="txt" label="${tool.name} on ${on_string} (narrowpeaks)">
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77 <filter>major_command['save_narrowpeak_file'] is True</filter>
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78 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom'</filter>
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79 </data>
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80 <data name="output_plot_file" format="pdf" label="${tool.name} on ${on_string} (plot)">
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81 <filter>major_command['save_plot_file'] is True</filter>
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82 </data>
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83 <data name="output_region_peak" format="txt" label="${tool.name} on ${on_string} (regionpeaks)">
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84 <filter>major_command['save_regionpeak_file'] is True</filter>
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85 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
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86 </data>
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87 <data name="output_peakshift_file" format="txt" label="${tool.name} on ${on_string} (peakshift/phantompeak)">
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88 <filter>major_command['save_peakshift_file'] is True</filter>
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89 <filter>major_command['major_command_selector'] == 'cross_correlation' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
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90 </data>
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91 <data name="output_rdata_file" format="txt" label="${tool.name} on ${on_string} (Rdata)">
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92 <filter>major_command['save_rdata_file'] is True</filter>
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93 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' </filter>
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94 </data>
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95 </outputs>
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96
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97 <configfiles>
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98 <configfile name="options_file"><%
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99 import simplejson
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100 %>
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101 #set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) }
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102
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103 #if str( $major_command.input_control_file1 ) != 'None':
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104 #set $__options['input_file'] = str( $major_command.input_control_file1 )
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105 #end if
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106
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107 ##=============================================================================
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108 #if str($major_command.major_command_selector) == 'cross_correlation':
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109 #set $__options['action'] = str( "cross_correlation" )
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110 #set $__options['rf'] = str( $major_command.replace )
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111
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112 #set $__options['out'] = str( $major_command.save_peakshift_file )
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113 #set $__options['savp'] = str( $major_command.save_plot_file )
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114 #end if
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115 ##=============================================================================
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116 #if str($major_command.major_command_selector) == 'peak_calling':
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117 #set $__options['action'] = str( "peak_calling" )
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118 #set $__options['fdr'] = str( $major_command.fdr )
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119 #set $__options['npeak'] = str( $major_command.num_peaks )
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120 #set $__options['rf'] = str( $major_command.replace )
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121
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122 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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123 #set $__options['savd'] = str( $major_command.save_rdata_file )
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124 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
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125 #set $__options['savp'] = str( $major_command.save_plot_file )
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126 #end if
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127 ##=============================================================================
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128 #if str($major_command.major_command_selector) == 'idr':
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129 #set $__options['action'] = str( "idr" )
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130 #set $__options['npeak'] = int( $major_command.num_peaks )
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131 #set $__options['rf'] = str( $major_command.replace )
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132
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133 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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134 #set $__options['out'] = str( $major_command.save_peakshift_file )
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135 #set $__options['savp'] = str( $major_command.save_plot_file )
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136 #end if
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137 ##=============================================================================
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138 #if str($major_command.major_command_selector) == 'custom':
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139 #set $__options['action'] = str( "custom" )
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140 #set $__options['s'] = str( $major_command.strand_shift )
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141 #set $__options['x'] = str( $major_command.excluded_strand_shift )
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142 #set $__options['npeak'] = int( $major_command.num_peaks )
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143 #set $__options['fdr'] = int( $major_command.fdr )
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144 #set $__options['rf'] = str( $major_command.replace )
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145
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146 #if str($major_command.user_defined_strpeak) == '':
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147 #set $__options['speak'] = str( $major_command.user_defined_strpeak )
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148 #else:
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149 #set $__options['speak'] = "-speak=$major_command.user_defined_strpeak"
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150 #end if
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151
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152 #if str($major_command.filter_char) == '':
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153 #set $__options['filtchr'] = str( $major_command.filter_char )
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154 #else:
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155 #set $__options['filtchr'] = "-filtchr=$major_command.filter_char"
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156 #end if
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157
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158 #set $__options['out'] = str( $major_command.save_peakshift_file )
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159 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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160 #set $__options['savd'] = str( $major_command.save_rdata_file )
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161 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
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162 #set $__options['savp'] = str( $major_command.save_plot_file )
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163 #end if
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164
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165 ${ simplejson.dumps( __options ) }
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166 </configfile>
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167 </configfiles>
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168 <tests>
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169 <!--none yet for spp-->
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170 </tests>
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171 <help>
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172 **What it does**
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173
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174 This tool allows ChIP-seq peak calling using SPP
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175
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176 This set of programs operate on mapped Illumina single-end read datasets in tagAlign or BAM format.
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177
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178 View the modified SPP documentation: http://code.google.com/p/phantompeakqualtools/
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179
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180 ------
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181
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182 **Usage**
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183
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184 **Determine strand cross-correlation peak**: Compute the predominant insert-size (fragment length) based on strand cross-correlation peak.
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185
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186 **Peak calling**: Call Peaks and regions for punctate binding datasets.
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187
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188 **IDR analysis**: Compute Data quality measures based on relative phantom peak.
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189
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190 **Custom settings**: Enables all options available to SPP for custom analysis.
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191
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192 ------
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193
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194 **Citation**
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195
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196 Anshul Kundaje, Computer Science Dept., Stanford University, ENCODE Consortium, Personal Communication, Oct 2010
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197 Kharchenko PK, Tolstorukov MY, Park PJ, Design and analysis of ChIP-seq experiments for DNA-binding proteins Nat Biotechnol. 2008 Dec;26(12):1351-9
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198
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199 Integration of SPP with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.
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200 </help>
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201 </tool>
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