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author modencode-dcc
date Fri, 18 Jan 2013 18:41:08 -0500
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4:ba5c7a2e64ff 5:b5c32b6c6a0b
1 <tool id="modencode_peakcalling_spp" name="SPP" version="1.10.1">
2 <requirements>
3 <requirement type="set_environment">SCRIPT_PATH</requirement>
4 </requirements>
5 <description>SPP cross-correlation analysis package</description>
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>
7 <inputs>
8 <!--experiment name and inputs-->
9 <param name="experiment_name" type="text" value="SPP in Galaxy" size="50" label="Experiment Name"/>
10
11 <!--select function to perform-->
12 <conditional name="major_command">
13 <param name="major_command_selector" type="select" label="Select action to be performed">
14 <option value="cross_correlation">Determine strand cross-correlation peak</option>
15 <option value="peak_calling">Peak calling</option>
16 <option value="idr">IDR analysis</option>
17 <option value="custom">Custom settings</option>
18 </param>
19 <when value="cross_correlation">
20 <!--cross correlation options-->
21 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
22 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
23
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)"/>
25
26 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
27 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
28 </when>
29 <when value="peak_calling">
30 <!--peak calling options-->
31 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
32 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
33
34 <param name="fdr" type="text" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
35 <param name="num_peaks" type="text" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
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)"/>
37
38 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file " help="(-savr)"/>
39 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="True" label="Save Rdata file" help="(-savd)"/>
40 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="True" label="Save narrowpeak file" help="(-savn)"/>
41 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
42 </when>
43 <when value="idr">
44 <!--idr options-->
45 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
46 <param name="input_control_file1" type="data" format="bam" label="ChIP-Seq Control File" />
47
48 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="300000" help="default=300000 (-npeak)"/>
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)"/>
50
51 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="True" label="Save regionpeak file" help="(-savr)"/>
52 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="True" label="Save peakshift file" help="(-out)"/>
53 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="True" label="Save plot file" help="(-savp)"/>
54 </when>
55 <when value="custom">
56 <!--custom settings, includes all relevant options here-->
57 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
58 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
59
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)"/>
61 <param name="excluded_strand_shift" type="text" label="Strand shifts to exclude" value="10:10" help="default=10:(readlen+10) (-x)"/>
62 <param name="user_defined_strpeak" type="text" label="User defined cross-correlation peak strand shift" help="(-speak)"/>
63 <param name="num_peaks" type="integer" label="Threshold on number of peaks to call" value="0" help="default=0 (-npeak)"/>
64 <param name="fdr" type="integer" label="False discovery rate threshold" value="0" help="default=0 (-fdr)"/>
65 <param name="filter_char" type="text" label="Pattern to use to remove tags that map to specific chromosomes" help="(-filtchr)"/>
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)"/>
67
68 <param name="save_regionpeak_file" truevalue="-savr" falsevalue="" type="boolean" checked="False" label="Save regionpeak file" help="(-savr)"/>
69 <param name="save_peakshift_file" truevalue="-out=peakshift.txt" falsevalue="" type="boolean" checked="False" label="Save peakshift file" help="(-out)"/>
70 <param name="save_rdata_file" truevalue="-savd" falsevalue="" type="boolean" checked="False" label="Save Rdata file" help="(-savd)"/>
71 <param name="save_narrowpeak_file" truevalue="-savn" falsevalue="" type="boolean" checked="False" label="Save narrowpeak file" help="(-savn)"/>
72 <param name="save_plot_file" truevalue="-savp" falsevalue="" type="boolean" checked="False" label="Save plot file" help="(-savp)"/>
73 </when>
74 </conditional>
75 </inputs>
76
77 <outputs>
78 <data name="output_default_file" format="txt" label="${tool.name} on ${on_string}"/>
79 <data name="output_narrow_peak" format="txt" label="${tool.name} on ${on_string} (narrowpeaks)">
80 <filter>major_command['save_narrowpeak_file'] is True</filter>
81 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom'</filter>
82 </data>
83 <data name="output_plot_file" format="pdf" label="${tool.name} on ${on_string} (plot)">
84 <filter>major_command['save_plot_file'] is True</filter>
85 </data>
86 <data name="output_region_peak" format="txt" label="${tool.name} on ${on_string} (regionpeaks)">
87 <filter>major_command['save_regionpeak_file'] is True</filter>
88 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
89 </data>
90 <data name="output_peakshift_file" format="txt" label="${tool.name} on ${on_string} (peakshift/phantompeak)">
91 <filter>major_command['save_peakshift_file'] is True</filter>
92 <filter>major_command['major_command_selector'] == 'cross_correlation' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' </filter>
93 </data>
94 <data name="output_rdata_file" format="txt" label="${tool.name} on ${on_string} (Rdata)">
95 <filter>major_command['save_rdata_file'] is True</filter>
96 <filter>major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' </filter>
97 </data>
98 </outputs>
99
100 <configfiles>
101 <configfile name="options_file">&lt;%
102 import simplejson
103 %&gt;
104 #set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) }
105
106 #if str( $major_command.input_control_file1 ) != 'None':
107 #set $__options['input_file'] = str( $major_command.input_control_file1 )
108 #end if
109
110 ##=============================================================================
111 #if str($major_command.major_command_selector) == 'cross_correlation':
112 #set $__options['action'] = str( "cross_correlation" )
113 #set $__options['rf'] = str( $major_command.replace )
114
115 #set $__options['out'] = str( $major_command.save_peakshift_file )
116 #set $__options['savp'] = str( $major_command.save_plot_file )
117 #end if
118 ##=============================================================================
119 #if str($major_command.major_command_selector) == 'peak_calling':
120 #set $__options['action'] = str( "peak_calling" )
121 #set $__options['fdr'] = str( $major_command.fdr )
122 #set $__options['npeak'] = str( $major_command.num_peaks )
123 #set $__options['rf'] = str( $major_command.replace )
124
125 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
126 #set $__options['savd'] = str( $major_command.save_rdata_file )
127 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
128 #set $__options['savp'] = str( $major_command.save_plot_file )
129 #end if
130 ##=============================================================================
131 #if str($major_command.major_command_selector) == 'idr':
132 #set $__options['action'] = str( "idr" )
133 #set $__options['npeak'] = int( $major_command.num_peaks )
134 #set $__options['rf'] = str( $major_command.replace )
135
136 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
137 #set $__options['out'] = str( $major_command.save_peakshift_file )
138 #set $__options['savp'] = str( $major_command.save_plot_file )
139 #end if
140 ##=============================================================================
141 #if str($major_command.major_command_selector) == 'custom':
142 #set $__options['action'] = str( "custom" )
143 #set $__options['s'] = str( $major_command.strand_shift )
144 #set $__options['x'] = str( $major_command.excluded_strand_shift )
145 #set $__options['npeak'] = int( $major_command.num_peaks )
146 #set $__options['fdr'] = int( $major_command.fdr )
147 #set $__options['rf'] = str( $major_command.replace )
148
149 #if str($major_command.user_defined_strpeak) == '':
150 #set $__options['speak'] = str( $major_command.user_defined_strpeak )
151 #else:
152 #set $__options['speak'] = "-speak=$major_command.user_defined_strpeak"
153 #end if
154
155 #if str($major_command.filter_char) == '':
156 #set $__options['filtchr'] = str( $major_command.filter_char )
157 #else:
158 #set $__options['filtchr'] = "-filtchr=$major_command.filter_char"
159 #end if
160
161 #set $__options['out'] = str( $major_command.save_peakshift_file )
162 #set $__options['savr'] = str( $major_command.save_regionpeak_file )
163 #set $__options['savd'] = str( $major_command.save_rdata_file )
164 #set $__options['savn'] = str( $major_command.save_narrowpeak_file )
165 #set $__options['savp'] = str( $major_command.save_plot_file )
166 #end if
167
168 ${ simplejson.dumps( __options ) }
169 </configfile>
170 </configfiles>
171 <tests>
172 <!--none yet for spp-->
173 </tests>
174 <help>
175 **What it does**
176
177 This tool allows ChIP-seq peak calling using SPP
178
179 This set of programs operate on mapped Illumina single-end read datasets in tagAlign or BAM format.
180
181 View the modified SPP documentation: http://code.google.com/p/phantompeakqualtools/
182
183 ------
184
185 **Usage**
186
187 **Determine strand cross-correlation peak**: Compute the predominant insert-size (fragment length) based on strand cross-correlation peak.
188
189 **Peak calling**: Call Peaks and regions for punctate binding datasets.
190
191 **IDR analysis**: Compute Data quality measures based on relative phantom peak.
192
193 **Custom settings**: Enables all options available to SPP for custom analysis.
194
195 ------
196
197 **Citation**
198
199 Anshul Kundaje, Computer Science Dept., Stanford University, ENCODE Consortium, Personal Communication, Oct 2010
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
201
202 Integration of SPP with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.
203 </help>
204 </tool>