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Replace simplejson with json. Add option to call broad peaks.
author stemcellcommons
date Tue, 20 May 2014 12:10:38 -0400
parents 642c0da30ca6
children
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0:642c0da30ca6 1:c05f607d116c
1 <tool id="macs2_peakcalling" name="MACS2" version="2.0.10"> 1 <tool id="macs2_peakcalling" name="MACS2" version="2.0.10">
2 <description>Model-based Analysis of ChIP-Seq</description> 2 <description>Model-based Analysis of ChIP-Seq</description>
3 <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command> 3 <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command>
4 <version_command>macs2 --version</version_command>
4 <inputs> 5 <inputs>
5 <!--experiment name and option of selecting paired or single end will always be present--> 6 <!--experiment name and option of selecting paired or single end will always be present-->
6 <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/> 7 <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/>
7 8
8 <!--select one of the 7 major commands offered by macs2--> 9 <!--select one of the 7 major commands offered by macs2-->
9 <conditional name="major_command"> 10 <conditional name="major_command">
10 <param name="major_command_selector" type="select" label="Select action to be performed"> 11 <param name="major_command_selector" type="select" label="Select action to be performed">
11 <option value="callpeak">Peak Calling</option> 12 <option value="callpeak">Peak Calling</option>
12 <!--<option value="filterdup">filterdup</option> 13 <!--<option value="filterdup">filterdup</option>
13 <option value="randsample">randsample</option>--> 14 <option value="randsample">randsample</option>-->
14 <option value="bdgcmp">Compare .bdg Files</option> 15 <option value="bdgcmp">Compare .bdg Files</option>
15 <!--<option value="bdgdiff">bdgdiff</option> 16 <!--<option value="bdgdiff">bdgdiff</option>
16 <option value="bdgpeakcall">bdgpeakcall</option> 17 <option value="bdgpeakcall">bdgpeakcall</option>
17 <option value="bdgbroadcall">bdgbroadcall</option>--> 18 <option value="bdgbroadcall">bdgbroadcall</option>-->
18 </param> 19 </param>
19 <!--callpeak option of macs2--> 20 <!--callpeak option of macs2-->
20 <when value="callpeak"> 21 <when value="callpeak">
21 <!--may need to add a few more formats at later time--> 22 <!--may need to add a few more formats at later time-->
22 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" /> 23 <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 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
24 <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)"/> 25 <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)"/>
25 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> 26 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/>
26 <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="True" falsevalue="False" checked="False"/> 27 <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="True" falsevalue="False" checked="False"/>
27 <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"/> 28 <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"/>
28 29
29 <conditional name="pq_options"> 30 <conditional name="pq_options">
30 <param name="pq_options_selector" type="select" label="Select p-value or q-value" help="default uses q-value"> 31 <param name="pq_options_selector" type="select" label="Select p-value or q-value" help="default uses q-value">
31 <option value="qvalue">q-value</option> 32 <option value="qvalue">q-value</option>
32 <option value="pvalue">p-value</option> 33 <option value="pvalue">p-value</option>
33 </param> 34 </param>
34 <when value="pvalue"> 35 <when value="pvalue">
35 <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="1e-2" help="default: 1e-2 (--pvalue)"/> 36 <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="1e-2" help="default: 1e-2 (--pvalue)"/>
36 </when> 37 </when>
37 <when value="qvalue"> 38 <when value="qvalue">
38 <param name="qvalue" type="float" label="q-value cutoff for peak detection" value="5e-2" help="default: 5e-2 (--qvalue)"/> 39 <param name="qvalue" type="float" label="q-value cutoff for peak detection" value="5e-2" help="default: 5e-2 (--qvalue)"/>
39 </when> 40 </when>
40 </conditional> 41 </conditional>
41 <conditional name="advanced_options"> 42 <conditional name="advanced_options">
42 <param name="advanced_options_selector" type="select" label="Display advanced options"> 43 <param name="advanced_options_selector" type="select" label="Display advanced options">
43 <option value="off">Hide</option> 44 <option value="off">Hide</option>
44 <option value="on">Display</option> 45 <option value="on">Display</option>
45 </param> 46 </param>
46 <when value="on"> 47 <when value="on">
47 <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)"/> 48 <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)"/>
48 <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)"/> 49 <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)"/>
49 <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)"/> 50 <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)"/>
50 </when> 51 <conditional name="broad_options">
51 <when value="off"> 52 <param name="broad_options_selector" type="select" label="Composite broad regions" help="put nearby highly enriched regions into a broad region with loose cutoff (--broad)">
52 <!--display nothing--> 53 <option value="nobroad" selected="true">No broad regions</option>
53 </when> 54 <option value="broad">Broad regions</option>
54 </conditional> 55 </param>
55 <conditional name="nomodel_type"> 56 <when value="broad">
57 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
58 </when>
59 <when value="nobroad"/>
60 </conditional>
61 </when>
62 <when value="off">
63 <!--display nothing-->
64 </when>
65 </conditional>
66 <conditional name="nomodel_type">
56 <param name="nomodel_type_selector" type="select" label="Build Model"> 67 <param name="nomodel_type_selector" type="select" label="Build Model">
57 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> 68 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option>
58 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> 69 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option>
59 </param> 70 </param>
60 <when value="nomodel"> 71 <when value="nomodel">
61 <param name="shiftsize" type="integer" label="Arbitrary shift size in bp" value="100" help="(--shiftsize)"/> 72 <param name="shiftsize" type="integer" label="Arbitrary shift size in bp" value="100" help="(--shiftsize)"/>
62 </when> 73 </when>
65 76
66 <!--callpeak option of macs2--> 77 <!--callpeak option of macs2-->
67 <when value="bdgcmp"> 78 <when value="bdgcmp">
68 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" /> 79 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" />
69 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" /> 80 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" />
70 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" help="default: 0.00001 (-p)"/> 81 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" help="default: 0.00001 (-p)"/>
71 82
72 <conditional name="bdgcmp_options"> 83 <conditional name="bdgcmp_options">
73 <param name="bdgcmp_options_selector" type="select" label="Select action to be performed"> 84 <param name="bdgcmp_options_selector" type="select" label="Select action to be performed">
74 <option value="ppois">ppois</option> 85 <option value="ppois">ppois</option>
75 <option value="qpois">qpois</option> 86 <option value="qpois">qpois</option>
76 <option value="subtract">subtract</option> 87 <option value="subtract">subtract</option>
77 <option value="logFE">logFE</option> 88 <option value="logFE">logFE</option>
78 <option value="FE">FE</option> 89 <option value="FE">FE</option>
79 <option value="logLR">logLR</option> 90 <option value="logLR">logLR</option>
80 </param> 91 </param>
81 </conditional> 92 </conditional>
82 </when> 93 </when>
83 </conditional> 94 </conditional>
84 </inputs> 95 </inputs>
85 96
86 <outputs> 97 <outputs>
112 </data> 123 </data>
113 </outputs> 124 </outputs>
114 <configfiles> 125 <configfiles>
115 126
116 <configfile name="outputs_file">&lt;% 127 <configfile name="outputs_file">&lt;%
117 import simplejson 128 import json
118 %&gt; 129 %&gt;
119 ##======================================================================================= 130 ##=======================================================================================
120 #set $__outputs = { 'command':str( $major_command.major_command_selector ) } 131 #set $__outputs = { 'command':str( $major_command.major_command_selector ) }
121 #if str( $major_command.major_command_selector ) == 'callpeak': 132 #if str( $major_command.major_command_selector ) == 'callpeak':
122 #set $__outputs['output_bed_file'] = str( $output_bed_file ) 133 #set $__outputs['output_bed_file'] = str( $output_bed_file )
123 #set $__outputs['output_extra_file'] = str( $output_extra_files ) 134 #set $__outputs['output_extra_file'] = str( $output_extra_files )
124 #set $__outputs['output_extra_file_path'] = str( $output_extra_files.files_path ) 135 #set $__outputs['output_extra_file_path'] = str( $output_extra_files.files_path )
125 #set $__outputs['output_peaks_file'] = str( $output_peaks_file ) 136 #set $__outputs['output_peaks_file'] = str( $output_peaks_file )
126 #set $__outputs['output_narrowpeaks_file'] = str( $output_narrowpeaks_file ) 137 #set $__outputs['output_narrowpeaks_file'] = str( $output_narrowpeaks_file )
127 #set $__outputs['output_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file ) 138 #set $__outputs['output_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file )
128 #set $__outputs['output_xls_to_interval_negative_peaks_file'] = str( $output_xls_to_interval_negative_peaks_file ) 139 #set $__outputs['output_xls_to_interval_negative_peaks_file'] = str( $output_xls_to_interval_negative_peaks_file )
129 #end if 140 #end if
130 ##======================================================================================= 141 ##=======================================================================================
131 #if str( $major_command.major_command_selector ) == 'bdgcmp': 142 #if str( $major_command.major_command_selector ) == 'bdgcmp':
132 #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file ) 143 #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file )
133 #end if 144 #end if
134 145
135 ${ simplejson.dumps( __outputs ) } 146 ${ json.dumps( __outputs ) }
136 </configfile> 147 </configfile>
137 <configfile name="options_file">&lt;% 148 <configfile name="options_file">&lt;%
138 import simplejson 149 import json
139 %&gt; 150 %&gt;
140 ##======================================================================================= 151 ##=======================================================================================
141 #set $__options = { 'experiment_name':str( $experiment_name ) } 152 #set $__options = { 'experiment_name':str( $experiment_name ) }
142 ##treatment/tag input files and format 153 ##treatment/tag input files and format
143 #set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ] 154 #set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ]
144 #set $__options['format'] = $major_command.input_chipseq_file1.extension.upper() 155 #set $__options['format'] = $major_command.input_chipseq_file1.extension.upper()
145 156
146 ##control/input files 157 ##control/input files
147 #set $__options['input_control'] = [] 158 #set $__options['input_control'] = []
148 #if str( $major_command.input_control_file1 ) != 'None': 159 #if str( $major_command.input_control_file1 ) != 'None':
149 #set $_hole = __options['input_control'].append( str( $major_command.input_control_file1 ) ) 160 #set $_hole = __options['input_control'].append( str( $major_command.input_control_file1 ) )
150 #end if 161 #end if
151 162
152 #if str( $major_command.major_command_selector ) == 'callpeak': 163 #if str( $major_command.major_command_selector ) == 'callpeak':
153 #set $__options['command'] = str( "callpeak" ) 164 #set $__options['command'] = str( "callpeak" )
154 #set $__options['gsize'] = int( $major_command.gsize ) 165 #set $__options['gsize'] = int( $major_command.gsize )
155 #set $__options['bw'] = str( $major_command.bw ) 166 #set $__options['bw'] = str( $major_command.bw )
156 #set $__options['bdg'] = str( $major_command.bdg ) 167 #set $__options['bdg'] = str( $major_command.bdg )
157 #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval ) 168 #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval )
158 169
159 ##advanced options 170 ##advanced options
160 #if str( $major_command.advanced_options.advanced_options_selector ) == 'on': 171 #if str( $major_command.advanced_options.advanced_options_selector ) == 'on':
161 #set $__options['mfoldlo'] = int( $major_command.advanced_options.mfoldlo ) 172 #set $__options['mfoldlo'] = int( $major_command.advanced_options.mfoldlo )
162 #set $__options['mfoldhi'] = int( $major_command.advanced_options.mfoldhi ) 173 #set $__options['mfoldhi'] = int( $major_command.advanced_options.mfoldhi )
163 #set $__options['nolambda'] = str( $major_command.advanced_options.nolambda ) 174 #set $__options['nolambda'] = str( $major_command.advanced_options.nolambda )
164 #else: 175 #if str($major_command.advanced_options.broad_options.broad_options_selector) == 'broad'
165 #set $__options['mfoldlo'] = int( "10" ) 176 #set $__options['broad_cutoff'] = str($major_command.advanced_options.broad_options.broad_cutoff)
166 #set $__options['mfoldhi'] = int( "30" ) 177 #end if
167 #set $__options['nolambda'] = str( "" ) 178 #else:
168 #end if 179 #set $__options['mfoldlo'] = int( "10" )
169 180 #set $__options['mfoldhi'] = int( "30" )
170 ##enable xls file options 181 #set $__options['nolambda'] = str( "" )
171 ##if str( $major_command.xls_to_interval ) == 'create': 182 #end if
172 ##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 ) } 183
173 ##end if 184 ##enable xls file options
174 185 ##if str( $major_command.xls_to_interval ) == 'create':
175 ##pq value select options 186 ##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 ) }
176 #if str( $major_command.pq_options.pq_options_selector ) == 'qvalue': 187 ##end if
177 #set $__options['qvalue'] = str( $major_command.pq_options.qvalue ) 188
178 #else: 189 ##pq value select options
179 #set $__options['pvalue'] = str( $major_command.pq_options.pvalue ) 190 #if str( $major_command.pq_options.pq_options_selector ) == 'qvalue':
180 #end if 191 #set $__options['qvalue'] = str( $major_command.pq_options.qvalue )
181 192 #else:
182 ##model options 193 #set $__options['pvalue'] = str( $major_command.pq_options.pvalue )
183 #if str( $major_command.nomodel_type.nomodel_type_selector ) == 'nomodel': 194 #end if
184 #set $__options['nomodel'] = str( $major_command.nomodel_type.shiftsize ) 195
185 #end if 196 ##model options
197 #if str( $major_command.nomodel_type.nomodel_type_selector ) == 'nomodel':
198 #set $__options['nomodel'] = str( $major_command.nomodel_type.shiftsize )
199 #end if
186 #end if 200 #end if
187 ##======================================================================================= 201 ##=======================================================================================
188 #if str( $major_command.major_command_selector ) == 'bdgcmp': 202 #if str( $major_command.major_command_selector ) == 'bdgcmp':
189 #set $__options['command'] = str( "bdgcmp" ) 203 #set $__options['command'] = str( "bdgcmp" )
190 #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) ) 204 #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) )
191 #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector ) 205 #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector )
192 #end if 206 #end if
193 ##======================================================================================= 207 ##=======================================================================================
194 208
195 ${ simplejson.dumps( __options ) } 209 ${ json.dumps( __options ) }
196 </configfile> 210 </configfile>
197 </configfiles> 211 </configfiles>
198 <tests> 212 <tests>
199 <!--none yet for macs2--> 213 <!--none yet for macs2-->
200 </tests> 214 </tests>
201 <help> 215 <help>
202 **What it does** 216 **What it does**
203 217
204 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) 218 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)