|
1
|
1 <tool id="modencode_peakcalling_spp" name="SPP" version="1.10.1">
|
|
|
2 <requirements>
|
|
|
3 <requirement type="set_environment">SCRIPT_PATH</requirement>
|
|
|
4 <!--<requirement type="package" version="1.16">peakranger</requirement>-->
|
|
|
5 </requirements>
|
|
|
6 <description>SPP cross-correlation analysis package</description>
|
|
|
7 <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>
|
|
|
8 <inputs>
|
|
|
9 <!--experiment name and inputs-->
|
|
|
10 <param name="experiment_name" type="text" value="SPP in Galaxy" size="50" label="Experiment Name"/>
|
|
|
11
|
|
|
12 <!--select function to perform-->
|
|
|
13 <conditional name="major_command">
|
|
|
14 <param name="major_command_selector" type="select" label="Select action to be performed">
|
|
|
15 <option value="cross_correlation">Determine strand cross-correlation peak</option>
|
|
|
16 <option value="peak_calling">Peak calling</option>
|
|
|
17 <option value="idr">IDR analysis</option>
|
|
|
18 <option value="custom">Custom settings</option>
|
|
|
19 </param>
|
|
|
20 <when value="cross_correlation">
|
|
|
21 <!--cross correlation options-->
|
|
|
22 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
|
|
|
23 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
|
|
|
24
|
|
|
25 <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)"/>
|
|
|
26
|
|
|
27 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
|
|
|
28 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
|
|
|
29 </when>
|
|
|
30 <when value="peak_calling">
|
|
|
31 <!--peak calling options-->
|
|
|
32 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
|
|
|
33 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
|
|
|
34
|
|
|
35 <param name="fdr" type="text" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
|
|
|
36 <param name="num_peaks" type="text" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
|
|
|
37 <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)"/>
|
|
|
38
|
|
|
39 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file " help="(-savr)"/>
|
|
|
40 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="True" label="Save Rdata file" help="(-savd)"/>
|
|
|
41 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="True" label="Save narrowpeak file" help="(-savn)"/>
|
|
|
42 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
|
|
|
43 </when>
|
|
|
44 <when value="idr">
|
|
|
45 <!--idr options-->
|
|
|
46 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
|
|
|
47 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
|
|
|
48
|
|
|
49 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="300000" help="default=300000 (-npeak)"/>
|
|
|
50 <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)"/>
|
|
|
51
|
|
|
52 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file" help="(-savr)"/>
|
|
|
53 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
|
|
|
54 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
|
|
|
55 </when>
|
|
|
56 <when value="custom">
|
|
|
57 <!--custom settings, includes all relevant options here-->
|
|
|
58 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
|
|
|
59 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
|
|
|
60
|
|
|
61 <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)"/>
|
|
|
62 <param name="excluded_strand_shift" type="text" label="Strand shifts to exclude" value="10:10" help="default=10:(readlen+10) (-x)"/>
|
|
|
63 <param name="user_defined_strpeak" type="text" label="User defined cross-correlation peak strand shift" help="(-speak)"/>
|
|
|
64 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
|
|
|
65 <param name="fdr" type="integer" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
|
|
|
66 <param name="filter_char" type="text" label="Pattern to use to remove tags that map to specific chromosomes" help="(-filtchr)"/>
|
|
|
67 <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)"/>
|
|
|
68
|
|
|
69 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="False" label="Save regionpeak file" help="(-savr)"/>
|
|
|
70 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="False" label="Save peakshift file" help="(-out)"/>
|
|
|
71 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="False" label="Save Rdata file" help="(-savd)"/>
|
|
|
72 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="False" label="Save narrowpeak file" help="(-savn)"/>
|
|
|
73 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="False" label="Save plot file" help="(-savp)"/>
|
|
|
74 </when>
|
|
|
75 </conditional>
|
|
|
76 </inputs>
|
|
|
77
|
|
|
78 <outputs>
|
|
|
79 <data name="output_default_file" format="txt" label="${tool.name} on ${on_string}"/>
|
|
|
80 <data name="output_narrow_peak" format="txt" label="${tool.name} on ${on_string} (narrowpeaks)">
|
|
|
81 <filter>major_command['save_narrowpeak_file'] is True</filter>
|
|
|
82 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom'</filter>
|
|
|
83 </data>
|
|
|
84 <data name="output_plot_file" format="pdf" label="${tool.name} on ${on_string} (plot)">
|
|
|
85 <filter>major_command['save_plot_file'] is True</filter>
|
|
|
86 </data>
|
|
|
87 <data name="output_region_peak" format="txt" label="${tool.name} on ${on_string} (regionpeaks)">
|
|
|
88 <filter>major_command['save_regionpeak_file'] is True</filter>
|
|
|
89 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
|
|
|
90 </data>
|
|
|
91 <data name="output_peakshift_file" format="txt" label="${tool.name} on ${on_string} (peakshift/phantompeak)">
|
|
|
92 <filter>major_command['save_peakshift_file'] is True</filter>
|
|
|
93 <filter>major_command['major_command_selector'] == 'cross_correlation' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
|
|
|
94 </data>
|
|
|
95 <data name="output_rdata_file" format="txt" label="${tool.name} on ${on_string} (Rdata)">
|
|
|
96 <filter>major_command['save_rdata_file'] is True</filter>
|
|
|
97 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' </filter>
|
|
|
98 </data>
|
|
|
99 </outputs>
|
|
|
100
|
|
|
101 <configfiles>
|
|
|
102 <configfile name="options_file"><%
|
|
|
103 import simplejson
|
|
|
104 %>
|
|
|
105 #set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) }
|
|
|
106
|
|
|
107 #if str( $major_command.input_control_file1 ) != 'None':
|
|
|
108 #set $__options['input_file'] = str( $major_command.input_control_file1 )
|
|
|
109 #end if
|
|
|
110
|
|
|
111 ##=============================================================================
|
|
|
112 #if str($major_command.major_command_selector) == 'cross_correlation':
|
|
|
113 #set $__options['action'] = str( "cross_correlation" )
|
|
|
114 #set $__options['rf'] = str( $major_command.replace )
|
|
|
115
|
|
|
116 #set $__options['out'] = str( $major_command.save_peakshift_file )
|
|
|
117 #set $__options['savp'] = str( $major_command.save_plot_file )
|
|
|
118 #end if
|
|
|
119 ##=============================================================================
|
|
|
120 #if str($major_command.major_command_selector) == 'peak_calling':
|
|
|
121 #set $__options['action'] = str( "peak_calling" )
|
|
|
122 #set $__options['fdr'] = str( $major_command.fdr )
|
|
|
123 #set $__options['npeak'] = str( $major_command.num_peaks )
|
|
|
124 #set $__options['rf'] = str( $major_command.replace )
|
|
|
125
|
|
|
126 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
|
|
|
127 #set $__options['savd'] = str( $major_command.save_rdata_file )
|
|
|
128 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
|
|
|
129 #set $__options['savp'] = str( $major_command.save_plot_file )
|
|
|
130 #end if
|
|
|
131 ##=============================================================================
|
|
|
132 #if str($major_command.major_command_selector) == 'idr':
|
|
|
133 #set $__options['action'] = str( "idr" )
|
|
|
134 #set $__options['npeak'] = int( $major_command.num_peaks )
|
|
|
135 #set $__options['rf'] = str( $major_command.replace )
|
|
|
136
|
|
|
137 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
|
|
|
138 #set $__options['out'] = str( $major_command.save_peakshift_file )
|
|
|
139 #set $__options['savp'] = str( $major_command.save_plot_file )
|
|
|
140 #end if
|
|
|
141 ##=============================================================================
|
|
|
142 #if str($major_command.major_command_selector) == 'custom':
|
|
|
143 #set $__options['action'] = str( "custom" )
|
|
|
144 #set $__options['s'] = str( $major_command.strand_shift )
|
|
|
145 #set $__options['x'] = str( $major_command.excluded_strand_shift )
|
|
|
146 #set $__options['npeak'] = int( $major_command.num_peaks )
|
|
|
147 #set $__options['fdr'] = int( $major_command.fdr )
|
|
|
148 #set $__options['rf'] = str( $major_command.replace )
|
|
|
149
|
|
|
150 #if str($major_command.user_defined_strpeak) == '':
|
|
|
151 #set $__options['speak'] = str( $major_command.user_defined_strpeak )
|
|
|
152 #else:
|
|
|
153 #set $__options['speak'] = "-speak=$major_command.user_defined_strpeak"
|
|
|
154 #end if
|
|
|
155
|
|
|
156 #if str($major_command.filter_char) == '':
|
|
|
157 #set $__options['filtchr'] = str( $major_command.filter_char )
|
|
|
158 #else:
|
|
|
159 #set $__options['filtchr'] = "-filtchr=$major_command.filter_char"
|
|
|
160 #end if
|
|
|
161
|
|
|
162 #set $__options['out'] = str( $major_command.save_peakshift_file )
|
|
|
163 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
|
|
|
164 #set $__options['savd'] = str( $major_command.save_rdata_file )
|
|
|
165 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
|
|
|
166 #set $__options['savp'] = str( $major_command.save_plot_file )
|
|
|
167 #end if
|
|
|
168
|
|
|
169 ${ simplejson.dumps( __options ) }
|
|
|
170 </configfile>
|
|
|
171 </configfiles>
|
|
|
172 <tests>
|
|
|
173 <!--none yet for spp-->
|
|
|
174 </tests>
|
|
|
175 <help>
|
|
|
176 **What it does**
|
|
|
177
|
|
|
178 This tool allows ChIP-seq peak calling using SPP
|
|
|
179
|
|
|
180 This set of programs operate on mapped Illumina single-end read datasets in tagAlign or BAM format.
|
|
|
181
|
|
|
182 View the modified SPP documentation: http://code.google.com/p/phantompeakqualtools/
|
|
|
183
|
|
|
184 ------
|
|
|
185
|
|
|
186 **Usage**
|
|
|
187
|
|
|
188 **Determine strand cross-correlation peak**: Compute the predominant insert-size (fragment length) based on strand cross-correlation peak.
|
|
|
189
|
|
|
190 **Peak calling**: Call Peaks and regions for punctate binding datasets.
|
|
|
191
|
|
|
192 **IDR analysis**: Compute Data quality measures based on relative phantom peak.
|
|
|
193
|
|
|
194 **Custom settings**: Enables all options available to SPP for custom analysis.
|
|
|
195
|
|
|
196 ------
|
|
|
197
|
|
|
198 **Citation**
|
|
|
199
|
|
|
200 Anshul Kundaje, Computer Science Dept., Stanford University, ENCODE Consortium, Personal Communication, Oct 2010
|
|
|
201 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
|
|
|
202
|
|
|
203 Integration of SPP with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.
|
|
|
204 </help>
|
|
|
205 </tool>
|
