annotate macs2_wrapper.xml @ 6:784f269a4c29 draft

Uploaded
author modencode-dcc
date Fri, 18 Jan 2013 11:24:29 -0500
parents 3cfa174db9f0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
1 <tool id="modencode_peakcalling_macs2" name="MACS2" version="2.0.10.2">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
2 <description>Model-based Analysis of ChIP-Seq</description>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
3 <!--<command interpreter="python">macs2_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path $output_peaks_file $output_narrowpeaks_file</command>-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
4 <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
5 <requirements>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
6 <requirement type="python-module">macs2</requirement>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
7 <requirement type="package">macs2</requirement>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
8 </requirements>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
9 <inputs>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
10 <!--experiment name and option of selecting paired or single end will always be present-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
11 <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
12
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
13 <!--select one of the 7 major commands offered by macs2-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
14 <conditional name="major_command">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
15 <param name="major_command_selector" type="select" label="Select action to be performed">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
16 <option value="callpeak">Peak Calling</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
17 <!--<option value="filterdup">filterdup</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
18 <option value="randsample">randsample</option>-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
19 <option value="bdgcmp">Compare .bdg Files</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
20 <!--<option value="bdgdiff">bdgdiff</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
21 <option value="bdgpeakcall">bdgpeakcall</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
22 <option value="bdgbroadcall">bdgbroadcall</option>-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
23 </param>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
24 <!--callpeak option of macs2-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
25 <when value="callpeak">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
26 <!--may need to add a few more formats at later time-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
27 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
28 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
29 <param name="gsize" type="float" label="Effective genome size" value="2.7e+9" help="Human: 3.3e+9, Mouse: 3.0e+9, Fly: 1.9e+8, Worm: 1.3e+8 (--gsize)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
30 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
31 <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="True" falsevalue="False" checked="False"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
32 <param name="bdg" label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" type="boolean" truevalue="-B" falsevalue="" checked="False" help="files located in html report"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
33
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
34 <conditional name="pq_options">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
35 <param name="pq_options_selector" type="select" label="Select p-value or q-value" help="default uses q-value">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
36 <option value="qvalue">q-value</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
37 <option value="pvalue">p-value</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
38 </param>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
39 <when value="pvalue">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
40 <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="1e-2" help="default: 1e-2 (--pvalue)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
41 </when>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
42 <when value="qvalue">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
43 <param name="qvalue" type="float" label="q-value cutoff for peak detection" value="5e-2" help="default: 5e-2 (--qvalue)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
44 </when>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
45 </conditional>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
46 <conditional name="advanced_options">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
47 <param name="advanced_options_selector" type="select" label="Display advanced options">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
48 <option value="off">Hide</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
49 <option value="on">Display</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
50 </param>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
51 <when value="on">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
52 <param name="mfoldlo" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" value="10" help="(--mfold)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
53 <param name="mfoldhi" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" value="30" help="(--mfold)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
54 <param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming (--nolambda)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
55 </when>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
56 <when value="off">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
57 <!--display nothing-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
58 </when>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
59 </conditional>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
60 <conditional name="nomodel_type">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
61 <param name="nomodel_type_selector" type="select" label="Build Model">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
62 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
63 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
64 </param>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
65 <when value="nomodel">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
66 <param name="shiftsize" type="integer" label="Arbitrary shift size in bp" value="100" help="(--shiftsize)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
67 </when>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
68 </conditional>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
69 </when>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
70
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
71 <!--callpeak option of macs2-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
72 <when value="bdgcmp">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
73 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
74 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
75 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" help="default: 0.00001 (-p)"/>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
76
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
77 <conditional name="bdgcmp_options">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
78 <param name="bdgcmp_options_selector" type="select" label="Select action to be performed">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
79 <option value="ppois">ppois</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
80 <option value="qpois">qpois</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
81 <option value="subtract">subtract</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
82 <option value="logFE">logFE</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
83 <option value="FE">FE</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
84 <option value="logLR">logLR</option>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
85 </param>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
86 </conditional>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
87 </when>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
88 </conditional>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
89 </inputs>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
90
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
91 <outputs>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
92 <!--callpeaks output-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
93 <data name="output_bed_file" format="bed" label="${tool.name}: callpeak on ${on_string} (peaks: bed)">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
94 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
95 </data>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
96 <data name="output_extra_files" format="html" label="${tool.name}: callpeak on ${on_string} (html report)">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
97 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
98 </data>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
99 <data name="output_peaks_file" format="xls" label="${tool.name}: callpeak on ${on_string} (peaks: xls)">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
100 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
101 </data>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
102 <data name="output_narrowpeaks_file" format="txt" label="${tool.name}: callpeak on ${on_string} (peaks: encodePeak)">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
103 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
104 </data>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
105 <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (peaks: interval)">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
106 <filter>major_command['xls_to_interval'] is True</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
107 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
108 </data>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
109 <data name="output_xls_to_interval_negative_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (negative peaks: interval)">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
110 <filter>major_command['xls_to_interval'] is True</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
111 <filter>major_command['input_control_file1'] is not None</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
112 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
113 </data>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
114 <!--bdgcmp output-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
115 <data name="output_bdgcmp_file" format="bdg" label="${tool.name}: bdgcmp on ${on_string} (bdg)">
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
116 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
117 </data>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
118 </outputs>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
119 <configfiles>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
120
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
121 <configfile name="outputs_file">&lt;%
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
122 import simplejson
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
123 %&gt;
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
124 ##=======================================================================================
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
125 #set $__outputs = { 'command':str( $major_command.major_command_selector ) }
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
126 #if str( $major_command.major_command_selector ) == 'callpeak':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
127 #set $__outputs['output_bed_file'] = str( $output_bed_file )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
128 #set $__outputs['output_extra_file'] = str( $output_extra_files )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
129 #set $__outputs['output_extra_file_path'] = str( $output_extra_files.files_path )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
130 #set $__outputs['output_peaks_file'] = str( $output_peaks_file )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
131 #set $__outputs['output_narrowpeaks_file'] = str( $output_narrowpeaks_file )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
132 #set $__outputs['output_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
133 #set $__outputs['output_xls_to_interval_negative_peaks_file'] = str( $output_xls_to_interval_negative_peaks_file )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
134 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
135 ##=======================================================================================
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
136 #if str( $major_command.major_command_selector ) == 'bdgcmp':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
137 #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
138 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
139
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
140 ${ simplejson.dumps( __outputs ) }
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
141 </configfile>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
142 <configfile name="options_file">&lt;%
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
143 import simplejson
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
144 %&gt;
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
145 ##=======================================================================================
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
146 #set $__options = { 'experiment_name':str( $experiment_name ) }
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
147 ##treatment/tag input files and format
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
148 #set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ]
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
149 #set $__options['format'] = $major_command.input_chipseq_file1.extension.upper()
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
150
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
151 ##control/input files
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
152 #set $__options['input_control'] = []
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
153 #if str( $major_command.input_control_file1 ) != 'None':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
154 #set $_hole = __options['input_control'].append( str( $major_command.input_control_file1 ) )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
155 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
156
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
157 #if str( $major_command.major_command_selector ) == 'callpeak':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
158 #set $__options['command'] = str( "callpeak" )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
159 #set $__options['gsize'] = int( $major_command.gsize )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
160 #set $__options['bw'] = str( $major_command.bw )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
161 #set $__options['bdg'] = str( $major_command.bdg )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
162 #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
163
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
164 ##advanced options
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
165 #if str( $major_command.advanced_options.advanced_options_selector ) == 'on':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
166 #set $__options['mfoldlo'] = int( $major_command.advanced_options.mfoldlo )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
167 #set $__options['mfoldhi'] = int( $major_command.advanced_options.mfoldhi )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
168 #set $__options['nolambda'] = str( $major_command.advanced_options.nolambda )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
169 #else:
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
170 #set $__options['mfoldlo'] = int( "10" )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
171 #set $__options['mfoldhi'] = int( "30" )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
172 #set $__options['nolambda'] = str( "" )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
173 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
174
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
175 ##enable xls file options
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
176 ##if str( $major_command.xls_to_interval ) == 'create':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
177 ##set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) }
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
178 ##end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
179
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
180 ##pq value select options
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
181 #if str( $major_command.pq_options.pq_options_selector ) == 'qvalue':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
182 #set $__options['qvalue'] = str( $major_command.pq_options.qvalue )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
183 #else:
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
184 #set $__options['pvalue'] = str( $major_command.pq_options.pvalue )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
185 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
186
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
187 ##model options
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
188 #if str( $major_command.nomodel_type.nomodel_type_selector ) == 'nomodel':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
189 #set $__options['nomodel'] = str( $major_command.nomodel_type.shiftsize )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
190 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
191 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
192 ##=======================================================================================
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
193 #if str( $major_command.major_command_selector ) == 'bdgcmp':
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
194 #set $__options['command'] = str( "bdgcmp" )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
195 #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
196 #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector )
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
197 #end if
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
198 ##=======================================================================================
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
199
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
200 ${ simplejson.dumps( __options ) }
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
201 </configfile>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
202 </configfiles>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
203 <tests>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
204 <!--none yet for macs2-->
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
205 </tests>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
206 <help>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
207 **What it does**
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
208
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
209 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
210 is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
211 identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
212 binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
213
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
214 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
215
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
216 ------
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
217
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
218 **Usage**
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
219
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
220 **Peak Calling**: Main MACS2 Function to Call peaks from alignment results.
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
221
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
222 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
223
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
224
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
225 ------
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
226
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
227 **Citation**
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
228
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
229 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
230
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
231 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
232 </help>
3cfa174db9f0 Uploaded
modencode-dcc
parents:
diff changeset
233 </tool>