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comparison ranger_wrapper.xml @ 10:6f56c88fc1d7 draft

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author modencode-dcc
date Thu, 17 Jan 2013 16:21:38 -0500
parents c983230e1ef8
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9:b3366931d056 10:6f56c88fc1d7
1 <tool id="modencode_peakcalling_ranger" name="PeakRanger" version="1.16">
2 <description>multi-purpose, ultrafast ChIP Seq peak caller</description>
3 <command interpreter="python">ranger_wrapper.py $options_file $outputs_file</command>
4 <requirements>
5 <requirement type="package">peakranger</requirement>
6 </requirements>
7 <inputs>
8 <param name="experiment_name" type="text" value="PeakRanger in Galaxy" size="50" label="Experiment Name"/>
9
10 <conditional name="major_command">
11 <param name="major_command_selector" type="select" label="Select action to be performed">
12 <option value="nr">Estimate data quality (nr)</option>
13 <option value="lc">Calculate library complexity (lc)</option>
14 <option value="wig">Generate coverage wiggle file (wig)</option>
15 <option value="wigpe">Generate coverage wiggle file using block models (wigpe)</option>
16 <option value="ranger">Peak calling for sharp peaks (ranger)</option>
17 <option value="ccat">Peak calling for broad peaks (ccat)</option>
18 </param>
19 <when value="nr">
20 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
21 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
22
23 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
24 </when>
25 <when value="lc">
26 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
27 </when>
28 <when value="wig">
29 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
30
31 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
32
33 <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="output will be in .zip format (-s)"/>
34 <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="output will be in .zip format (-x)"/>
35 <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
36 </when>
37 <when value="wigpe">
38 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
39
40 <param name="extension" type="integer" value="0" label="Read extension length" help="default=0 (-l)"/>
41
42 <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="(-s)"/>
43 <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="(-x)"/>
44 <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
45 </when>
46 <when value="ranger">
47 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
48 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
49
50 <conditional name="gene_annotate_file">
51 <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
52 <option value="dm3refGene.txt">dm3refGene.txt</option>
53 <option value="hg19refGene.txt">hg19refGene.txt</option>
54 <option value="mm9refGene.txt">mm9refGene.txt</option>
55 <option value="Upload">Select from history</option>
56 <option value="None">None</option>
57 </param>
58 <when value="upload">
59 <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
60 </when>
61 </conditional>
62 <param name="threads" type="integer" value="1" label="Number of threads" help="default=1 (-t)"/>
63 <param name="plot_region" type="integer" value="6000" label="The length of the snapshot region in the HTML report" help="(--plot_region)"/>
64 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
65 <param name="pvalue" type="float" value="0.0001" label="p-value cut-off" help="default=0.0001 (-p)"/>
66 <param name="fdr" type="float" value="0.01" label="FDR cut-off" help="default=0.01 (-p)"/>
67 <param name="delta" type="integer" value="1" label="Sensitivity of the summit detector" help="default=1 (-r)"/>
68 <param name="bandwith" type="integer" value="99" label="Smoothing bandwith" help="default=99 (-b)"/>
69
70 <param name="pad" truevalue="--pad" falsevalue="" type="boolean" checked="False" label="Pad read coverage profile to avoid false positive summits" help="(--pad)"/>
71 </when>
72 <when value="ccat">
73 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
74 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
75
76 <conditional name="gene_annotate_file">
77 <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
78 <option value="dm3refGene.txt">dm3refGene.txt</option>
79 <option value="hg19refGene.txt">hg19refGene.txt</option>
80 <option value="mm9refGene.txt">mm9refGene.txt</option>
81 <option value="Upload">Select from history</option>
82 <option value="None">None</option>
83 </param>
84 <when value="upload">
85 <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
86 </when>
87 </conditional>
88 <param name="plot_region" type="integer" value="6000" label="Read extension length" help="default=6000 (--plot_region)"/>
89 <param name="extension" type="integer" value="100" label="Read extension length" help="default=100 (-l)"/>
90 <param name="fdr" type="float" value="0.11" label="FDR cut-off" help="default=0.11 (-q)"/>
91 <param name="winsize" type="integer" value="500" label="Sliding window size" help="default=500 (--win_size)"/>
92 <param name="winstep" type="integer" value="50" label="Window moving step" help="default=50 (--win_step)"/>
93 <param name="mincount" type="integer" value="4" label="Minimum window reads count" help="default=4 (--min_count)"/>
94 <param name="minscore" type="integer" value="5" label="Minimum window reads fold change" help="default=5 (--min_score)"/>
95 </when>
96 </conditional>
97 </inputs>
98
99 <outputs>
100 <data name="output_ranger_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
101 <filter>major_command['major_command_selector'] == 'nr' or major_command['major_command_selector'] == 'lc' or major_command['major_command_selector'] == 'ccat'</filter>
102 </data>
103 <data name="output_wigzip_file" format="wig, zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
104 <filter>major_command['major_command_selector'] == 'wig' or major_command['major_command_selector'] == 'wigpe'</filter>
105 </data>
106 <data name="output_summit_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (summit)">
107 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
108 </data>
109 <data name="output_region_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (region)">
110 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
111 </data>
112 <data name="output_details_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (details)">
113 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
114 </data>
115 <data name="output_report_file" format="zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (html report)">
116 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
117 <filter>major_command['gene_annotate_file']['gene_annotate_file_selector'] != 'None'</filter>
118 </data>
119 </outputs>
120
121 <configfiles>
122 <configfile name="outputs_file">&lt;%
123 import simplejson
124 %&gt;
125 ##=======================================================================================
126 #set $__outputs = { 'command':str( $major_command.major_command_selector ) }
127 #if str( $major_command.major_command_selector ) == 'nr' or str( $major_command.major_command_selector ) == 'lc':
128 #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
129 #end if
130 ##=======================================================================================
131 #if str( $major_command.major_command_selector ) == 'wig' or str( $major_command.major_command_selector ) == 'wigpe':
132 #set $__outputs['output_wigzip_file'] = str( $output_wigzip_file )
133 #end if
134 ##=======================================================================================
135 #if str( $major_command.major_command_selector ) == 'ranger' or str( $major_command.major_command_selector ) == 'ccat':
136 #set $__outputs['output_summit_file'] = str( $output_summit_file )
137 #set $__outputs['output_region_file'] = str( $output_region_file )
138 #set $__outputs['output_details_file'] = str( $output_details_file )
139 #set $__outputs['output_report_file'] = str( $output_report_file )
140 #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
141 #end if
142 ##=======================================================================================
143 ${ simplejson.dumps( __outputs ) }
144 </configfile>
145 <configfile name="options_file">&lt;%
146 import simplejson
147 %&gt;
148 #set $__options = { 'experiment_name':str($experiment_name), 'action':str( $major_command.major_command_selector ) }
149
150 ##=============================================================================
151 #if str($major_command.major_command_selector) == 'nr':
152 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
153 #set $__options['input_file'] = str( $major_command.input_control_file1 )
154
155 #set $__options['extension'] = str( $major_command.extension )
156 #end if
157 ##=============================================================================
158 ##if str($major_command.major_command_selector) == 'lc':
159 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
160 ##end if
161 ##=============================================================================
162 #if str($major_command.major_command_selector) == 'wig' or str($major_command.major_command_selector) == 'wigpe':
163 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
164
165 #set $__options['extension'] = str( $major_command.extension )
166 #set $__options['split'] = str( $major_command.split )
167 #set $__options['strand'] = str( $major_command.strand)
168 #set $__options['gzip'] = str( $major_command.gzip )
169 #end if
170 ##=============================================================================
171 #if str($major_command.major_command_selector) == 'ranger':
172 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
173 #set $__options['input_file'] = str( $major_command.input_control_file1 )
174
175 #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
176 #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
177 #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file )
178 #end if
179
180 #set $__options['plot_region'] = str( $major_command.plot_region )
181 #set $__options['pvalue'] = str( $major_command.pvalue )
182 #set $__options['fdr'] = str( $major_command.fdr )
183 #set $__options['extension'] = str( $major_command.extension )
184 #set $__options['delta'] = str( $major_command.delta )
185 #set $__options['threads'] = str( $major_command.threads )
186 #set $__options['bandwith'] = str( $major_command.bandwith )
187 #set $__options['pad'] = str( $major_command.pad )
188 #end if
189 ##=============================================================================
190 #if str($major_command.major_command_selector) == 'ccat':
191 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
192 #set $__options['input_file'] = str( $major_command.input_control_file1 )
193
194 #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
195 #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
196 #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file )
197 #end if
198
199 #set $__options['plot_region'] = str( $major_command.plot_region )
200 #set $__options['fdr'] = str( $major_command.fdr )
201 #set $__options['extension'] = str( $major_command.extension )
202 #set $__options['winsize'] = str( $major_command.winsize )
203 #set $__options['winstep'] = str( $major_command.winstep )
204 #set $__options['mincount'] = str( $major_command.mincount )
205 #set $__options['minscore'] = str( $major_command.minscore )
206 #end if
207 ##=============================================================================
208 ${ simplejson.dumps( __options ) }
209 </configfile>
210 </configfiles>
211 <tests>
212 <!--none yet for macs2-->
213 </tests>
214 <help>
215 **What it does**
216
217 PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:
218
219 View the modified PeakRanger documentation: http://ranger.sourceforge.net/manualv116.html#introduction
220
221 ------
222
223 **Usage**
224
225 **nr:** noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment
226
227 **lc:** library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.
228
229 **wig:** coverage file generator. Generates variable step format wiggle file
230
231 **wigpe:** coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files
232
233 wigpe can also generate coverage files for bam files containing spliced reads, such as those from RNA-Seq experiments.
234
235 **ranger:** ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.
236
237 **ccat:** ChIP-Seq peak caller. Tuned for the discovery of broad peaks
238
239 Both ranger and ccat supports generating HTML-based annotation reports.
240
241 ------
242
243 **Citation**
244
245 If you use PeakRanger in your research, please cite:
246 Feng X, Grossman R, Stein L: PeakRanger:A cloud-enabled peak caller for ChIP-seq data.BMC Bioinformatics 2011, 12(1):139.
247
248 if you use the ccat tool, please also cite:
249 Xu, H., L. Handoko, et al. (2010).A signal-noise model for significance analysis of ChIP-seq with negative control.Bioinformatics 26(9): 1199-1204.
250
251
252 Integration of PeakRanger with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.
253 </help>
254 </tool>