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comparison ranger_wrapper.xml @ 18:18a7ae54c2e0 draft

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author modencode-dcc
date Mon, 21 Jan 2013 14:01:02 -0500
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17:d2319b4df472 18:18a7ae54c2e0
1 <tool id="modencode_peakcalling_ranger" name="PeakRanger" version="1.16">
2 <requirements>
3 <requirement type="set_environment">SCRIPT_PATH</requirement>
4 <requirement type="package" version="1.16">peakranger</requirement>
5 </requirements>
6 <description>multi-purpose, ultrafast ChIP Seq peak caller</description>
7 <command interpreter="python">ranger_wrapper.py $options_file $outputs_file \$SCRIPT_PATH</command>
8 <inputs>
9 <param name="experiment_name" type="text" value="PeakRanger in Galaxy" size="50" label="Experiment Name"/>
10
11 <conditional name="major_command">
12 <param name="major_command_selector" type="select" label="Select action to be performed">
13 <option value="nr">Estimate data quality (nr)</option>
14 <option value="lc">Calculate library complexity (lc)</option>
15 <option value="wig">Generate coverage wiggle file (wig)</option>
16 <option value="wigpe">Generate coverage wiggle file using block models (wigpe)</option>
17 <option value="ranger">Peak calling for sharp peaks (ranger)</option>
18 <option value="ccat">Peak calling for broad peaks (ccat)</option>
19 </param>
20 <when value="nr">
21 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
22 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
23
24 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
25 </when>
26 <when value="lc">
27 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
28 </when>
29 <when value="wig">
30 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
31
32 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
33
34 <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)"/>
35 <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)"/>
36 <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
37 </when>
38 <when value="wigpe">
39 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
40
41 <param name="extension" type="integer" value="0" label="Read extension length" help="default=0 (-l)"/>
42
43 <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="(-s)"/>
44 <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="(-x)"/>
45 <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>
46 </when>
47 <when value="ranger">
48 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
49 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
50
51 <conditional name="gene_annotate_file">
52 <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
53 <option value="dm3refGene.txt">dm3refGene.txt</option>
54 <option value="hg19refGene.txt">hg19refGene.txt</option>
55 <option value="mm9refGene.txt">mm9refGene.txt</option>
56 <option value="Upload">Select from history</option>
57 <option value="None">None</option>
58 </param>
59 <when value="upload">
60 <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
61 </when>
62 </conditional>
63 <param name="threads" type="integer" value="1" label="Number of threads" help="default=1 (-t)"/>
64 <param name="plot_region" type="integer" value="6000" label="The length of the snapshot region in the HTML report" help="(--plot_region)"/>
65 <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>
66 <param name="pvalue" type="float" value="0.0001" label="p-value cut-off" help="default=0.0001 (-p)"/>
67 <param name="fdr" type="float" value="0.01" label="FDR cut-off" help="default=0.01 (-p)"/>
68 <param name="delta" type="integer" value="1" label="Sensitivity of the summit detector" help="default=1 (-r)"/>
69 <param name="bandwith" type="integer" value="99" label="Smoothing bandwith" help="default=99 (-b)"/>
70
71 <param name="pad" truevalue="--pad" falsevalue="" type="boolean" checked="False" label="Pad read coverage profile to avoid false positive summits" help="(--pad)"/>
72 </when>
73 <when value="ccat">
74 <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />
75 <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />
76
77 <conditional name="gene_annotate_file">
78 <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">
79 <option value="dm3refGene.txt">dm3refGene.txt</option>
80 <option value="hg19refGene.txt">hg19refGene.txt</option>
81 <option value="mm9refGene.txt">mm9refGene.txt</option>
82 <option value="Upload">Select from history</option>
83 <option value="None">None</option>
84 </param>
85 <when value="upload">
86 <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />
87 </when>
88 </conditional>
89 <param name="plot_region" type="integer" value="6000" label="Read extension length" help="default=6000 (--plot_region)"/>
90 <param name="extension" type="integer" value="100" label="Read extension length" help="default=100 (-l)"/>
91 <param name="fdr" type="float" value="0.11" label="FDR cut-off" help="default=0.11 (-q)"/>
92 <param name="winsize" type="integer" value="500" label="Sliding window size" help="default=500 (--win_size)"/>
93 <param name="winstep" type="integer" value="50" label="Window moving step" help="default=50 (--win_step)"/>
94 <param name="mincount" type="integer" value="4" label="Minimum window reads count" help="default=4 (--min_count)"/>
95 <param name="minscore" type="integer" value="5" label="Minimum window reads fold change" help="default=5 (--min_score)"/>
96 </when>
97 </conditional>
98 </inputs>
99
100 <outputs>
101 <data name="output_ranger_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
102 <filter>major_command['major_command_selector'] == 'nr' or major_command['major_command_selector'] == 'lc' or major_command['major_command_selector'] == 'ccat'</filter>
103 </data>
104 <data name="output_wigzip_file" format="wig, zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string}">
105 <filter>major_command['major_command_selector'] == 'wig' or major_command['major_command_selector'] == 'wigpe'</filter>
106 </data>
107 <data name="output_summit_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (summit)">
108 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
109 </data>
110 <data name="output_region_file" format="bed" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (region)">
111 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
112 </data>
113 <data name="output_details_file" format="txt" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (details)">
114 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
115 </data>
116 <data name="output_report_file" format="zip" label="${tool.name}: ${major_command.major_command_selector} on ${on_string} (html report)">
117 <filter>major_command['major_command_selector'] == 'ranger' or major_command['major_command_selector'] == 'ccat'</filter>
118 <filter>major_command['gene_annotate_file']['gene_annotate_file_selector'] != 'None'</filter>
119 </data>
120 </outputs>
121
122 <configfiles>
123 <configfile name="outputs_file">&lt;%
124 import simplejson
125 %&gt;
126 ##=======================================================================================
127 #set $__outputs = { 'command':str( $major_command.major_command_selector ) }
128 #if str( $major_command.major_command_selector ) == 'nr' or str( $major_command.major_command_selector ) == 'lc':
129 #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
130 #end if
131 ##=======================================================================================
132 #if str( $major_command.major_command_selector ) == 'wig' or str( $major_command.major_command_selector ) == 'wigpe':
133 #set $__outputs['output_wigzip_file'] = str( $output_wigzip_file )
134 #end if
135 ##=======================================================================================
136 #if str( $major_command.major_command_selector ) == 'ranger' or str( $major_command.major_command_selector ) == 'ccat':
137 #set $__outputs['output_summit_file'] = str( $output_summit_file )
138 #set $__outputs['output_region_file'] = str( $output_region_file )
139 #set $__outputs['output_details_file'] = str( $output_details_file )
140 #set $__outputs['output_report_file'] = str( $output_report_file )
141 #set $__outputs['output_ranger_file'] = str( $output_ranger_file )
142 #end if
143 ##=======================================================================================
144 ${ simplejson.dumps( __outputs ) }
145 </configfile>
146 <configfile name="options_file">&lt;%
147 import simplejson
148 %&gt;
149 #set $__options = { 'experiment_name':str($experiment_name), 'action':str( $major_command.major_command_selector ) }
150
151 ##=============================================================================
152 #if str($major_command.major_command_selector) == 'nr':
153 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
154 #set $__options['input_file'] = str( $major_command.input_control_file1 )
155
156 #set $__options['extension'] = str( $major_command.extension )
157 #end if
158 ##=============================================================================
159 ##if str($major_command.major_command_selector) == 'lc':
160 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
161 ##end if
162 ##=============================================================================
163 #if str($major_command.major_command_selector) == 'wig' or str($major_command.major_command_selector) == 'wigpe':
164 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
165
166 #set $__options['extension'] = str( $major_command.extension )
167 #set $__options['split'] = str( $major_command.split )
168 #set $__options['strand'] = str( $major_command.strand)
169 #set $__options['gzip'] = str( $major_command.gzip )
170 #end if
171 ##=============================================================================
172 #if str($major_command.major_command_selector) == 'ranger':
173 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
174 #set $__options['input_file'] = str( $major_command.input_control_file1 )
175
176 #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
177 #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
178 #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file )
179 #end if
180
181 #set $__options['plot_region'] = str( $major_command.plot_region )
182 #set $__options['pvalue'] = str( $major_command.pvalue )
183 #set $__options['fdr'] = str( $major_command.fdr )
184 #set $__options['extension'] = str( $major_command.extension )
185 #set $__options['delta'] = str( $major_command.delta )
186 #set $__options['threads'] = str( $major_command.threads )
187 #set $__options['bandwith'] = str( $major_command.bandwith )
188 #set $__options['pad'] = str( $major_command.pad )
189 #end if
190 ##=============================================================================
191 #if str($major_command.major_command_selector) == 'ccat':
192 #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )
193 #set $__options['input_file'] = str( $major_command.input_control_file1 )
194
195 #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )
196 #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'
197 #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file )
198 #end if
199
200 #set $__options['plot_region'] = str( $major_command.plot_region )
201 #set $__options['fdr'] = str( $major_command.fdr )
202 #set $__options['extension'] = str( $major_command.extension )
203 #set $__options['winsize'] = str( $major_command.winsize )
204 #set $__options['winstep'] = str( $major_command.winstep )
205 #set $__options['mincount'] = str( $major_command.mincount )
206 #set $__options['minscore'] = str( $major_command.minscore )
207 #end if
208 ##=============================================================================
209 ${ simplejson.dumps( __options ) }
210 </configfile>
211 </configfiles>
212 <tests>
213 <!--none yet for macs2-->
214 </tests>
215 <help>
216 **What it does**
217
218 PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:
219
220 View the modified PeakRanger documentation: http://ranger.sourceforge.net/manualv116.html#introduction
221
222 ------
223
224 **Usage**
225
226 **nr:** noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment
227
228 **lc:** library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.
229
230 **wig:** coverage file generator. Generates variable step format wiggle file
231
232 **wigpe:** coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files
233
234 wigpe can also generate coverage files for bam files containing spliced reads, such as those from RNA-Seq experiments.
235
236 **ranger:** ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.
237
238 **ccat:** ChIP-Seq peak caller. Tuned for the discovery of broad peaks
239
240 Both ranger and ccat supports generating HTML-based annotation reports.
241
242 ------
243
244 **Citation**
245
246 If you use PeakRanger in your research, please cite:
247 Feng X, Grossman R, Stein L: PeakRanger:A cloud-enabled peak caller for ChIP-seq data.BMC Bioinformatics 2011, 12(1):139.
248
249 if you use the ccat tool, please also cite:
250 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.
251
252
253 Integration of PeakRanger with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.
254 </help>
255 </tool>