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comparison ccat_wrapper.xml @ 0:a0c8dc671a23 draft

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:27:03 -0500
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children 201d8e7dfc43
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1 <tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
2 <description>Control-based ChIP-seq Analysis Tool</description>
3 <requirements>
4 <requirement type="package" version="3.0">CCAT</requirement>
5 </requirements>
6 <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo'
7 #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
8 '$input_advanced_config_file'
9 #else:
10 '${ options_type.input_config_file.fields.path }'
11 #end if
12 'CCAT in Galaxy'
13 '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command>
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="advanced" />
91 <param name="fragment_size" value="200" />
92 <param name="sliding_window_size" value="500" />
93 <param name="moving_step" value="50" />
94 <param name="is_strand_sensitive_mode" value="0" />
95 <param name="min_count" value="4" />
96 <param name="output_num" value="100000" />
97 <param name="random_seed" value="123456" />
98 <param name="min_score" value="5.0" />
99 <param name="bootstrap_pass" value="50" />
100 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
101 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
102 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />
103 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
104 </test>
105 <test>
106 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
107 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
108 <param name="options_type_selector" value="basic" />
109 <param name="input_config_file" value="ccat_3.0_histone_config" />
110 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
111 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
112 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
113 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
114 </test>
115 <!-- Test below gives different answers on different architectures,
116 e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386
117 slidingWinSize was fixed to be 1000, default as per readme.txt
118 -->
119 <!--
120 <test>
121 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
122 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
123 <param name="options_type_selector" value="basic" />
124 <param name="input_config_file" value="ccat_3.0_histone_config_readme" />
125 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />
126 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />
127 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" />
128 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />
129 </test>
130 -->
131 </tests>
132 <help>
133 **What it does**
134
135 This tool allows ChIP-seq peak/region calling using CCAT.
136
137 View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.
138
139 ------
140
141 **Citation**
142
143 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
144
145 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
146
147 </help>
148 </tool>