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1 <tool id="modencode_peakcalling_spp" name="SPP" version="1.10.1">
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2 <requirements>
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3 <requirement type="set_environment">SCRIPT_PATH</requirement>
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4 </requirements>
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5 <description>SPP cross-correlation analysis package</description>
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6 <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 \$SCRIPT_PATH</command>
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7 <inputs>
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8 <!--experiment name and inputs-->
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9 <param name="experiment_name" type="text" value="SPP in Galaxy" size="50" label="Experiment Name"/>
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10
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11 <!--select function to perform-->
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12 <conditional name="major_command">
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13 <param name="major_command_selector" type="select" label="Select action to be performed">
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14 <option value="cross_correlation">Determine strand cross-correlation peak</option>
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15 <option value="peak_calling">Peak calling</option>
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16 <option value="idr">IDR analysis</option>
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17 <option value="custom">Custom settings</option>
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18 </param>
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19 <when value="cross_correlation">
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20 <!--cross correlation options-->
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21 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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22 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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23
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24 <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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25
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26 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
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27 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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28 </when>
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29 <when value="peak_calling">
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30 <!--peak calling options-->
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31 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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32 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
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33
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34 <param name="fdr" type="text" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
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35 <param name="num_peaks" type="text" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
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36 <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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37
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38 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file " help="(-savr)"/>
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39 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="True" label="Save Rdata file" help="(-savd)"/>
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40 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="True" label="Save narrowpeak file" help="(-savn)"/>
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41 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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42 </when>
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43 <when value="idr">
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44 <!--idr options-->
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45 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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46 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
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47
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48 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="300000" help="default=300000 (-npeak)"/>
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49 <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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50
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51 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file" help="(-savr)"/>
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52 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
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53 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
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54 </when>
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55 <when value="custom">
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56 <!--custom settings, includes all relevant options here-->
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57 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
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58 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
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59
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60 <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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61 <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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62 <param name="user_defined_strpeak" type="text" label="User defined cross-correlation peak strand shift" help="(-speak)"/>
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63 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
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64 <param name="fdr" type="integer" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
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65 <param name="filter_char" type="text" label="Pattern to use to remove tags that map to specific chromosomes" help="(-filtchr)"/>
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66 <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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67
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68 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="False" label="Save regionpeak file" help="(-savr)"/>
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69 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="False" label="Save peakshift file" help="(-out)"/>
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70 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="False" label="Save Rdata file" help="(-savd)"/>
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71 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="False" label="Save narrowpeak file" help="(-savn)"/>
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72 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="False" label="Save plot file" help="(-savp)"/>
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73 </when>
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74 </conditional>
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75 </inputs>
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76
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77 <outputs>
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78 <data name="output_default_file" format="txt" label="${tool.name} on ${on_string}"/>
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79 <data name="output_narrow_peak" format="txt" label="${tool.name} on ${on_string} (narrowpeaks)">
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80 <filter>major_command['save_narrowpeak_file'] is True</filter>
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81 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom'</filter>
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82 </data>
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83 <data name="output_plot_file" format="pdf" label="${tool.name} on ${on_string} (plot)">
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84 <filter>major_command['save_plot_file'] is True</filter>
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85 </data>
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86 <data name="output_region_peak" format="txt" label="${tool.name} on ${on_string} (regionpeaks)">
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87 <filter>major_command['save_regionpeak_file'] is True</filter>
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88 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
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89 </data>
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90 <data name="output_peakshift_file" format="txt" label="${tool.name} on ${on_string} (peakshift/phantompeak)">
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91 <filter>major_command['save_peakshift_file'] is True</filter>
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92 <filter>major_command['major_command_selector'] == 'cross_correlation' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
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93 </data>
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94 <data name="output_rdata_file" format="txt" label="${tool.name} on ${on_string} (Rdata)">
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95 <filter>major_command['save_rdata_file'] is True</filter>
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96 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' </filter>
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97 </data>
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98 </outputs>
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99
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100 <configfiles>
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101 <configfile name="options_file"><%
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102 import simplejson
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103 %>
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104 #set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) }
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105
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106 #if str( $major_command.input_control_file1 ) != 'None':
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107 #set $__options['input_file'] = str( $major_command.input_control_file1 )
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108 #end if
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109
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110 ##=============================================================================
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111 #if str($major_command.major_command_selector) == 'cross_correlation':
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112 #set $__options['action'] = str( "cross_correlation" )
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113 #set $__options['rf'] = str( $major_command.replace )
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114
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115 #set $__options['out'] = str( $major_command.save_peakshift_file )
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116 #set $__options['savp'] = str( $major_command.save_plot_file )
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117 #end if
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118 ##=============================================================================
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119 #if str($major_command.major_command_selector) == 'peak_calling':
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120 #set $__options['action'] = str( "peak_calling" )
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121 #set $__options['fdr'] = str( $major_command.fdr )
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122 #set $__options['npeak'] = str( $major_command.num_peaks )
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123 #set $__options['rf'] = str( $major_command.replace )
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124
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125 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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126 #set $__options['savd'] = str( $major_command.save_rdata_file )
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127 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
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128 #set $__options['savp'] = str( $major_command.save_plot_file )
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129 #end if
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130 ##=============================================================================
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131 #if str($major_command.major_command_selector) == 'idr':
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132 #set $__options['action'] = str( "idr" )
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133 #set $__options['npeak'] = int( $major_command.num_peaks )
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134 #set $__options['rf'] = str( $major_command.replace )
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135
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136 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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137 #set $__options['out'] = str( $major_command.save_peakshift_file )
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138 #set $__options['savp'] = str( $major_command.save_plot_file )
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139 #end if
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140 ##=============================================================================
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141 #if str($major_command.major_command_selector) == 'custom':
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142 #set $__options['action'] = str( "custom" )
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143 #set $__options['s'] = str( $major_command.strand_shift )
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144 #set $__options['x'] = str( $major_command.excluded_strand_shift )
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145 #set $__options['npeak'] = int( $major_command.num_peaks )
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146 #set $__options['fdr'] = int( $major_command.fdr )
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147 #set $__options['rf'] = str( $major_command.replace )
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148
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149 #if str($major_command.user_defined_strpeak) == '':
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150 #set $__options['speak'] = str( $major_command.user_defined_strpeak )
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151 #else:
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152 #set $__options['speak'] = "-speak=$major_command.user_defined_strpeak"
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153 #end if
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154
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155 #if str($major_command.filter_char) == '':
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156 #set $__options['filtchr'] = str( $major_command.filter_char )
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157 #else:
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158 #set $__options['filtchr'] = "-filtchr=$major_command.filter_char"
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159 #end if
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160
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161 #set $__options['out'] = str( $major_command.save_peakshift_file )
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162 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
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163 #set $__options['savd'] = str( $major_command.save_rdata_file )
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164 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
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165 #set $__options['savp'] = str( $major_command.save_plot_file )
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166 #end if
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167
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168 ${ simplejson.dumps( __options ) }
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169 </configfile>
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170 </configfiles>
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171 <tests>
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172 <!--none yet for spp-->
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173 </tests>
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174 <help>
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175 **What it does**
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176
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177 This tool allows ChIP-seq peak calling using SPP
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178
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179 This set of programs operate on mapped Illumina single-end read datasets in tagAlign or BAM format.
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180
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181 View the modified SPP documentation: http://code.google.com/p/phantompeakqualtools/
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182
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183 ------
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184
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185 **Usage**
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186
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187 **Determine strand cross-correlation peak**: Compute the predominant insert-size (fragment length) based on strand cross-correlation peak.
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188
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189 **Peak calling**: Call Peaks and regions for punctate binding datasets.
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190
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191 **IDR analysis**: Compute Data quality measures based on relative phantom peak.
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192
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193 **Custom settings**: Enables all options available to SPP for custom analysis.
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194
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195 ------
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196
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197 **Citation**
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198
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199 Anshul Kundaje, Computer Science Dept., Stanford University, ENCODE Consortium, Personal Communication, Oct 2010
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200 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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201
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202 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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203 </help>
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204 </tool> |
