|
19
|
1 <tool id="peakcalling_ccat" name="CCAT" version="0.1">
|
|
|
2 <description>Control-based ChIP-seq Analysis Tool</description>
|
|
|
3 <requirements>
|
|
|
4 <container type="docker">institutcuriengsintegration/ccat:1.0</container>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$genome'
|
|
|
7 #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
|
|
|
8 '$input_advanced_config_file'
|
|
|
9 #else:
|
|
|
10 $options_type[ 'input_config_file' ]
|
|
|
11 #end if
|
|
|
12 'CCAT'
|
|
|
13 '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file' '${__root_dir__}'</command>
|
|
|
14 <inputs>
|
|
|
15 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" />
|
|
|
16 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" />
|
|
|
17 <param name="genome" type="select" label="Genome" >
|
|
|
18 <option value="hg19" selected="True">Human (hg19)</option>
|
|
|
19 <option value="mm10" >Mouse (mm10)</option>
|
|
|
20 <option value="hg18" >Human (hg18)</option>
|
|
|
21 <option value="mm9" >Mouse (mm9)</option>
|
|
|
22 </param>
|
|
|
23 <conditional name="options_type">
|
|
|
24 <param name="options_type_selector" type="select" label="Advanced Options">
|
|
|
25 <option value="basic" selected="True">Hide Advanced Options and select configuration file</option>
|
|
|
26 <option value="advanced">Show Advanced Options</option>
|
|
|
27 </param>
|
|
|
28 <when value="basic">
|
|
|
29 <param name="input_config_file" type="data" format="txt" label="Select a pre-defined configuration file" />
|
|
|
30 </when>
|
|
|
31 <when value="advanced">
|
|
|
32 <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
|
|
|
33 <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
|
|
|
34 <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
|
|
|
35 <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
|
|
|
36 <option value="1">Transition from sense strand to anti-sense strand</option>
|
|
|
37 <option value="0" selected="True">Local maximum of read-enrichment profile</option>
|
|
|
38 </param>
|
|
|
39 <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
|
|
|
40 <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
|
|
|
41 <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
|
|
|
42 <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
|
|
|
43 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
|
|
|
44 </when>
|
|
|
45 </conditional>
|
|
|
46 </inputs>
|
|
|
47 <outputs>
|
|
|
48 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
|
|
|
49 <actions>
|
|
|
50 <action type="metadata" name="chromCol" default="1"/>
|
|
|
51 <action type="metadata" name="startCol" default="3"/>
|
|
|
52 <action type="metadata" name="endCol" default="4"/>
|
|
|
53 </actions>
|
|
|
54 </data>
|
|
|
55 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
|
|
|
56 <actions>
|
|
|
57 <action type="metadata" name="chromCol" default="1"/>
|
|
|
58 <action type="metadata" name="startCol" default="3"/>
|
|
|
59 <action type="metadata" name="endCol" default="4"/>
|
|
|
60 </actions>
|
|
|
61 </data>
|
|
|
62 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
|
|
|
63 <actions>
|
|
|
64 <action type="metadata" name="chromCol" default="1"/>
|
|
|
65 <action type="metadata" name="startCol" default="3"/>
|
|
|
66 <action type="metadata" name="endCol" default="4"/>
|
|
|
67 </actions>
|
|
|
68 </data>
|
|
|
69 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
|
|
|
70 </outputs>
|
|
|
71 <configfiles>
|
|
|
72 <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
|
|
|
73 fragmentSize ${options_type[ 'fragment_size' ]}
|
|
|
74 slidingWinSize ${options_type[ 'sliding_window_size' ]}
|
|
|
75 movingStep ${options_type[ 'moving_step' ]}
|
|
|
76 isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]}
|
|
|
77 minCount ${options_type[ 'min_count' ]}
|
|
|
78 outputNum ${options_type[ 'output_num' ]}
|
|
|
79 randomSeed ${options_type[ 'random_seed' ]}
|
|
|
80 minScore ${options_type[ 'min_score' ]}
|
|
|
81 bootstrapPass ${options_type[ 'bootstrap_pass' ]}
|
|
|
82 #end if</configfile>
|
|
|
83 </configfiles>
|
|
|
84 <help>
|
|
|
85 **What it does**
|
|
|
86
|
|
|
87 This tool allows ChIP-seq peak/region calling using CCAT.
|
|
|
88
|
|
|
89 View the original CCAT `documentation. <http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.html>`_
|
|
|
90
|
|
|
91 ------
|
|
|
92
|
|
|
93 **Citation**
|
|
|
94
|
|
|
95 For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. <http://www.ncbi.nlm.nih.gov/pubmed/20371496>`_
|
|
|
96
|
|
|
97 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
|
|
|
98
|
|
|
99 </help>
|
|
|
100 </tool>
|
