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annotate spp_wrapper.xml @ 0:d4236b60701f draft default tip

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planemo upload for repository https://github.com/eba2016/spp_tool commit 2fb169b136aea9887da7ab9fdccc442443f8efa3-dirty
author gandres
date Wed, 25 May 2016 11:52:21 -0400
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0
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1 <tool id="modencode_peakcalling_spp" name="SPP" version="1.13.0">
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2 <description>SPP cross-correlation analysis package</description>
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3 <requirements>
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4 <requirement type="set_environment">SCRIPT_PATH</requirement>
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5 <requirement type="package" version="1.13">spp</requirement>
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6 </requirements>
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7 <command>python $__tool_directory__/spp_wrapper.py $options_file $output_narrow_peak $output_region_peak $output_peakshift_file $output_rdata_file $output_plot_file $output_default_file \$SCRIPT_PATH</command>
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8 <configfiles>
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9 <configfile name="options_file">&lt;%
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10 import simplejson
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11 %&gt;
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12 #set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) }
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13
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14 #if str( $major_command.input_control_file1 ) != 'None':
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15 #set $__options['input_file'] = str( $major_command.input_control_file1 )
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16 #end if
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18 ##=============================================================================
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19 #if str($major_command.major_command_selector) == 'cross_correlation':
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20 #set $__options['action'] = str( "cross_correlation" )
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21
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22 #set $__options['out'] = str( $major_command.save_peakshift_file )
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23 #set $__options['savp'] = str( $major_command.save_plot_file )
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24 #end if
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25 ##=============================================================================
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26 #if str($major_command.major_command_selector) == 'peak_calling':
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27 #set $__options['action'] = str( "peak_calling" )
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28 #set $__options['fdr'] = str( $major_command.fdr )
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29 #set $__options['npeak'] = str( $major_command.num_peaks )
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30
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31 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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32 #set $__options['savd'] = str( $major_command.save_rdata_file )
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33 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
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34 #set $__options['savp'] = str( $major_command.save_plot_file )
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35 #end if
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36 ##=============================================================================
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37 #if str($major_command.major_command_selector) == 'idr':
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38 #set $__options['action'] = str( "idr" )
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39 #set $__options['npeak'] = int( $major_command.num_peaks )
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40
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41 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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42 #set $__options['out'] = str( $major_command.save_peakshift_file )
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43 #set $__options['savp'] = str( $major_command.save_plot_file )
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44 #end if
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45 ##=============================================================================
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46 #if str($major_command.major_command_selector) == 'custom':
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47 #set $__options['action'] = str( "custom" )
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48 #set $__options['s'] = str( $major_command.strand_shift )
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49 #set $__options['x'] = str( $major_command.excluded_strand_shift )
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50 #set $__options['npeak'] = int( $major_command.num_peaks )
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51 #set $__options['fdr'] = int( $major_command.fdr )
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52
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53 #if str($major_command.user_defined_strpeak) == '':
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54 #set $__options['speak'] = str( $major_command.user_defined_strpeak )
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55 #else:
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56 #set $__options['speak'] = "-speak=$major_command.user_defined_strpeak"
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57 #end if
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58
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59 #if str($major_command.filter_char) == '':
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60 #set $__options['filtchr'] = str( $major_command.filter_char )
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61 #else:
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62 #set $__options['filtchr'] = "-filtchr=$major_command.filter_char"
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63 #end if
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64
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65 #set $__options['out'] = str( $major_command.save_peakshift_file )
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66 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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67 #set $__options['savd'] = str( $major_command.save_rdata_file )
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68 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
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69 #set $__options['savp'] = str( $major_command.save_plot_file )
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70 #end if
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71
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72 ${ simplejson.dumps( __options ) }
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73 </configfile>
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74 </configfiles>
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75
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76 <inputs>
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77 <!--experiment name and inputs-->
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78 <param name="experiment_name" type="text" value="SPP in Galaxy" size="50" label="Experiment Name"/>
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79
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80 <!--select function to perform-->
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81 <conditional name="major_command">
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82 <param name="major_command_selector" type="select" label="Select action to be performed">
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83 <option value="cross_correlation">Determine strand cross-correlation peak</option>
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84 <option value="peak_calling">Peak calling</option>
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85 <option value="idr">IDR analysis</option>
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86 <option value="custom">Custom settings</option>
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87 </param>
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88 <when value="cross_correlation">
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89 <!--cross correlation options-->
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90 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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91 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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92
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93
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94 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
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95 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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96 </when>
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97 <when value="peak_calling">
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98 <!--peak calling options-->
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99 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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100 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
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101
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102 <param name="fdr" type="text" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
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103 <param name="num_peaks" type="text" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
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104
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105 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file " help="(-savr)"/>
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106 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="True" label="Save Rdata file" help="(-savd)"/>
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107 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="True" label="Save narrowpeak file" help="(-savn)"/>
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108 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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109 </when>
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110 <when value="idr">
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111 <!--idr options-->
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112 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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113 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
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114
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115 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="300000" help="default=300000 (-npeak)"/>
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116
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117 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file" help="(-savr)"/>
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118 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
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119 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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120 </when>
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121 <when value="custom">
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122 <!--custom settings, includes all relevant options here-->
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123 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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124 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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125
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126 <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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127 <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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128 <param name="user_defined_strpeak" type="text" label="User defined cross-correlation peak strand shift" help="(-speak)"/>
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129 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
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130 <param name="fdr" type="integer" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
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131 <param name="filter_char" type="text" label="Pattern to use to remove tags that map to specific chromosomes" help="(-filtchr)"/>
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132
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133 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="False" label="Save regionpeak file" help="(-savr)"/>
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134 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="False" label="Save peakshift file" help="(-out)"/>
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135 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="False" label="Save Rdata file" help="(-savd)"/>
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136 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="False" label="Save narrowpeak file" help="(-savn)"/>
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137 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="False" label="Save plot file" help="(-savp)"/>
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138 </when>
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139 </conditional>
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140 </inputs>
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141
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142 <outputs>
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143 <data name="output_default_file" format="txt" label="${tool.name}-${major_command.major_command_selector} on ${on_string}"/>
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144 <data name="output_narrow_peak" format="txt" label="${tool.name}-${major_command.major_command_selector} on ${on_string} (narrowpeaks)">
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145 <filter>major_command['save_narrowpeak_file'] is True</filter>
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146 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom'</filter>
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147 </data>
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148 <data name="output_plot_file" format="pdf" label="${tool.name}-${major_command.major_command_selector} on ${on_string} (plot)">
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149 <filter>major_command['save_plot_file'] is True</filter>
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150 </data>
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151 <data name="output_region_peak" format="txt" label="${tool.name}-${major_command.major_command_selector} on ${on_string} (regionpeaks)">
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152 <filter>major_command['save_regionpeak_file'] is True</filter>
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153 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
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154 </data>
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155 <data name="output_peakshift_file" format="txt" label="${tool.name}-${major_command.major_command_selector} on ${on_string} (peakshift/phantompeak)">
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156 <filter>major_command['save_peakshift_file'] is True</filter>
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157 <filter>major_command['major_command_selector'] == 'cross_correlation' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
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158 </data>
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159 <data name="output_rdata_file" format="txt" label="${tool.name}-${major_command.major_command_selector} on ${on_string} (Rdata)">
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160 <filter>major_command['save_rdata_file'] is True</filter>
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161 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' </filter>
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162 </data>
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163 </outputs>
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164
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165 <tests>
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166 <!--none yet for spp-->
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167 <test>
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168 <param name="major_command_selector" value="cross_correlation"/>
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169 <param name="input_chipseq_file1" value="tag_file.bam"/>
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170 <param name="input_control_file1" value="control_file.bam"/>
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171 <output name="output_peakshift_file">
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172 <assert_contents>
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173 <has_line_matching expression="^.*\t192996\t100\t0.552186886771392\t45\t0.4766414\t600\t0.1428672\t3.865035\t1.226337\t1$" />
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174 <has_n_columns n="11" />
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175 </assert_contents>
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176 </output>
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177 <output name="output_default_file">
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178 <assert_contents>
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179 <has_line line="done. read 192996 fragments" />
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180 <has_line line="ChIP data read length 37 " />
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181 <has_line line="Minimum cross-correlation value 0.1428672 " />
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182 <has_line line="Peak cross-correlation value 0.552186886771392 " />
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183 <has_line line="Peak strand shift 100 " />
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184 <has_line line="Window half size 260 " />
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185 <has_line line="Phantom peak location 45 " />
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186 <has_line line="Phantom peak Correlation 0.4766414 " />
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187 <has_line line="Normalized cross-correlation coefficient (NCCC) 3.865035 " />
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188 <has_line line="Relative Cross correlation Coefficient (RCCC) 1.226337 " />
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189 <has_line line="Phantom Peak Quality Tag 1 " />
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190 </assert_contents>
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191 </output>
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192 </test>
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193 <test>
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194 <param name="major_command_selector" value="cross_correlation"/>
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195 <param name="input_chipseq_file1" value="tag_file.bam"/>
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196 <output name="output_peakshift_file">
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197 <assert_contents>
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198 <has_line_matching expression="^.*\t192996\t100\t0.552186886771392\t45\t0.4766414\t600\t0.1428672\t3.865035\t1.226337\t1$" />
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199 <has_n_columns n="11" />
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200 </assert_contents>
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201 </output>
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202 </test>
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203 </tests>
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204 <help>
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205 **What it does**
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206
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207 This tool allows ChIP-seq peak calling using SPP
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208
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209 This set of programs operate on mapped Illumina single-end read datasets in tagAlign or BAM format.
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210
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211 View the modified SPP documentation: http://code.google.com/p/phantompeakqualtools/
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212
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213 ------
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214
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215 **Usage**
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216
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217 **Determine strand cross-correlation peak**: Compute the predominant insert-size (fragment length) based on strand cross-correlation peak.
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218
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219 **Peak calling**: Call Peaks and regions for punctate binding datasets.
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220
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221 **IDR analysis**: Compute Data quality measures based on relative phantom peak.
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222
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223 **Custom settings**: Enables all options available to SPP for custom analysis.
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224
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225 ------
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226
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227 **Output**
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228
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229
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230 The column names of narrow- and region-peaks datasets (produced by **Peak calling**) are provided below:
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231
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232 - col 1: chrom
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233 - col 2: start
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234 - col 3: end
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235 - col 4: name
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236 - col 5: score
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237 - col 6: strand
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238 - col 7: signalValue
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239 - col 8 : -1
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240 - col 9: -log10(fdr)
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241 - col 10: Point-source called for this peak.
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242
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243 ------
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244
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245
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246 **Citation**
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247
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248 Anshul Kundaje, Computer Science Dept., Stanford University, ENCODE Consortium, Personal Communication, Oct 2010
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249 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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250
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251 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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252 </help>
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253 <citations>
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254 <citation type="doi">doi:10.1038/nbt.1508</citation>
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255 </citations>
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256 </tool>