Mercurial > repos > xuebing > sharplabtool
comparison tools/peak_calling/ccat_2_wrapper.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="peakcalling_ccat2" name="CCAT" version="0.0.1"> | |
2 <description>Control-based ChIP-seq Analysis Tool</description> | |
3 <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' | |
4 #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': | |
5 '$input_advanced_config_file' | |
6 #else: | |
7 '${ options_type.input_config_file.fields.path }' | |
8 #end if | |
9 'CCAT in Galaxy' | |
10 '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> | |
11 <requirements> | |
12 <requirement type="binary">CCAT</requirement> | |
13 </requirements> | |
14 <inputs> | |
15 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > | |
16 <validator type="unspecified_build" /> | |
17 </param> | |
18 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > | |
19 <validator type="unspecified_build" /> | |
20 </param> | |
21 <conditional name="options_type"> | |
22 <param name="options_type_selector" type="select" label="Advanced Options"> | |
23 <option value="basic" selected="True">Hide Advanced Options</option> | |
24 <option value="advanced">Show Advanced Options</option> | |
25 </param> | |
26 <when value="basic"> | |
27 <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> | |
28 <options from_data_table="ccat_configurations"> | |
29 <validator type="no_options" message="No configurations are available"/> | |
30 </options> | |
31 </param> | |
32 </when> | |
33 <when value="advanced"> | |
34 <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> | |
35 <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> | |
36 <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> | |
37 <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > | |
38 <option value="1">Transition from sense strand to anti-sense strand</option> | |
39 <option value="0" selected="True">Local maximum of read-enrichment profile</option> | |
40 </param> | |
41 <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> | |
42 <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> | |
43 <param name="random_seed" type="integer" label="Random Seed" value="123456"/> | |
44 <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> | |
45 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> | |
46 </when> | |
47 </conditional> | |
48 </inputs> | |
49 <outputs> | |
50 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> | |
51 <actions> | |
52 <action type="metadata" name="chromCol" default="1"/> | |
53 <action type="metadata" name="startCol" default="3"/> | |
54 <action type="metadata" name="endCol" default="4"/> | |
55 </actions> | |
56 </data> | |
57 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> | |
58 <actions> | |
59 <action type="metadata" name="chromCol" default="1"/> | |
60 <action type="metadata" name="startCol" default="3"/> | |
61 <action type="metadata" name="endCol" default="4"/> | |
62 </actions> | |
63 </data> | |
64 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> | |
65 <actions> | |
66 <action type="metadata" name="chromCol" default="1"/> | |
67 <action type="metadata" name="startCol" default="3"/> | |
68 <action type="metadata" name="endCol" default="4"/> | |
69 </actions> | |
70 </data> | |
71 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> | |
72 </outputs> | |
73 <configfiles> | |
74 <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': | |
75 fragmentSize ${options_type[ 'fragment_size' ]} | |
76 slidingWinSize ${options_type[ 'sliding_window_size' ]} | |
77 movingStep ${options_type[ 'moving_step' ]} | |
78 isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} | |
79 minCount ${options_type[ 'min_count' ]} | |
80 outputNum ${options_type[ 'output_num' ]} | |
81 randomSeed ${options_type[ 'random_seed' ]} | |
82 minScore ${options_type[ 'min_score' ]} | |
83 bootstrapPass ${options_type[ 'bootstrap_pass' ]} | |
84 #end if</configfile> | |
85 </configfiles> | |
86 <tests> | |
87 <test> | |
88 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> | |
89 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> | |
90 <param name="options_type_selector" value="basic" /> | |
91 <param name="input_config_file" value="ccat_2.0_histone_config" /> | |
92 <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> | |
93 <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> | |
94 <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> | |
95 <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> | |
96 </test> | |
97 <test> | |
98 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> | |
99 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> | |
100 <param name="options_type_selector" value="advanced" /> | |
101 <param name="fragment_size" value="200" /> | |
102 <param name="sliding_window_size" value="500" /> | |
103 <param name="moving_step" value="50" /> | |
104 <param name="is_strand_sensitive_mode" value="0" /> | |
105 <param name="min_count" value="4" /> | |
106 <param name="output_num" value="100000" /> | |
107 <param name="random_seed" value="123456" /> | |
108 <param name="min_score" value="3.0" /> | |
109 <param name="bootstrap_pass" value="50" /> | |
110 <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> | |
111 <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> | |
112 <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> | |
113 <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> | |
114 </test> | |
115 </tests> | |
116 <help> | |
117 **What it does** | |
118 | |
119 This tool allows ChIP-seq peak/region calling using CCAT. | |
120 | |
121 View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. | |
122 </help> | |
123 </tool> |