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comparison sicer_wrapper.xml @ 0:82a8234e03f2 draft

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:28:33 -0500
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-1:000000000000 0:82a8234e03f2
1 <tool id="peakcalling_sicer" name="SICER" version="0.0.1">
2 <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
3 <command interpreter="python">sicer_wrapper.py
4 --bed_file '${input_bed_file}'
5 #if str( $input_control_file ) != 'None':
6 --control_file '${input_control_file}'
7 --significant_islands_output_file "${significant_islands_output_file}"
8 --islands_summary_output_file "${islands_summary_output_file}"
9 --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
10 #end if
11 ${fix_off_by_one_errors}
12 --dbkey '${input_bed_file.dbkey}'
13 --redundancy_threshold '${redundancy_threshold}'
14 --window_size '${window_size}'
15 --fragment_size '${fragment_size}'
16 --effective_genome_fraction '${effective_genome_fraction}'
17 --gap_size '${gap_size}'
18 --error_cut_off '${error_cut_off}'
19 ##output files
20 --stdout "${output_log_file}"
21 --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
22 --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
23 --score_island_output_file "${score_island_output_file}"
24 --summary_graph_output_file "${summary_graph_output_file}"
25 --test_normalized_wig_output_file "${test_normalized_wig_output_file}"
26 --island_filtered_output_file "${island_filtered_output_file}"
27 --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
28 </command>
29 <requirements>
30 <requirement type="package" version="1.1">SICER</requirement>
31 </requirements>
32 <inputs>
33 <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
34 <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator>
35 </param>
36 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys -->
37 <options>
38 <filter type="data_meta" ref="input_bed_file" key="dbkey" />
39 </options>
40 </param>
41 <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="True" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/>
42 <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
43 <param name="window_size" type="integer" label="Window size" value="200" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
44 <param name="fragment_size" type="integer" label="Fragment size" value="150" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />
45 <param name="effective_genome_fraction" type="float" label="Effective genome fraction" value="0.74" help="Effective Genome as fraction of the genome size. It depends on read length." />
46 <param name="gap_size" type="integer" label="Gap size" value="600" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
47 <param name="error_cut_off" type="float" label="Statistic threshold value" value="0.01" help="FDR (with control) or E-value (without control)" />
48 </inputs>
49 <outputs>
50 <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
51 <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
52 <filter>input_control_file is not None</filter>
53 </data>
54 <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
55 <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
56 <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
57 <filter>input_control_file is not None</filter>
58 </data>
59 <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
60 <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
61 <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/>
62 <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
63 <filter>input_control_file is not None</filter>
64 </data>
65 <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
66 <filter>input_control_file is not None</filter>
67 </data>
68 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
69 </outputs>
70 <tests>
71 <test>
72 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
73 <param name="input_control_file" />
74 <param name="fix_off_by_one_errors" />
75 <param name="redundancy_threshold" value="1" />
76 <param name="window_size" value="200" />
77 <param name="fragment_size" value="150" />
78 <param name="effective_genome_fraction" value="0.74" />
79 <param name="gap_size" value="600" />
80 <param name="error_cut_off" value="0.01" />
81 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />
82 <output name="summary_graph_output_file" file="peakcalling_sicer/test_1/test-W200.graph" />
83 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />
84 <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />
85 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />
86 <output name="score_island_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland" />
87 <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>
88 </test>
89 <test>
90 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
91 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
92 <param name="fix_off_by_one_errors" />
93 <param name="redundancy_threshold" value="1" />
94 <param name="window_size" value="200" />
95 <param name="fragment_size" value="150" />
96 <param name="effective_genome_fraction" value="0.74" />
97 <param name="gap_size" value="600" />
98 <param name="error_cut_off" value="0.01" />
99 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />
100 <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />
101 <output name="summary_graph_output_file" file="peakcalling_sicer/test_2/test-W200.graph" />
102 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />
103 <output name="significant_islands_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed" />
104 <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />
105 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
106 <output name="score_island_output_file" file="peakcalling_sicer/test_2/test-W200-G600.scoreisland" />
107 <output name="islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary" />
108 <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01" />
109 <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>
110 </test>
111 <test>
112 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
113 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
114 <param name="fix_off_by_one_errors" value="True" />
115 <param name="redundancy_threshold" value="1" />
116 <param name="window_size" value="200" />
117 <param name="fragment_size" value="150" />
118 <param name="effective_genome_fraction" value="0.74" />
119 <param name="gap_size" value="600" />
120 <param name="error_cut_off" value="0.01" />
121 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />
122 <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />
123 <output name="summary_graph_output_file" file="peakcalling_sicer/test_3/test-W200.graph" />
124 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />
125 <output name="significant_islands_output_file" file="peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed" />
126 <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />
127 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
128 <output name="score_island_output_file" file="peakcalling_sicer/test_3/test-W200-G600.scoreisland" />
129 <output name="islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary" />
130 <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01" />
131 <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>
132 </test>
133 <test>
134 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
135 <param name="input_control_file" />
136 <param name="fix_off_by_one_errors" value="True" />
137 <param name="redundancy_threshold" value="1" />
138 <param name="window_size" value="200" />
139 <param name="fragment_size" value="150" />
140 <param name="effective_genome_fraction" value="0.74" />
141 <param name="gap_size" value="600" />
142 <param name="error_cut_off" value="0.01" />
143 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />
144 <output name="summary_graph_output_file" file="peakcalling_sicer/test_4/test-W200.graph" />
145 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />
146 <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />
147 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />
148 <output name="score_island_output_file" file="peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland" />
149 <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>
150 </test>
151 </tests>
152 <help>
153 **What it does**
154
155 SICER first and foremost is a filtering tool. Its main functions are::
156
157 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks.
158 2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.
159
160 View the original SICER documentation: http://home.gwu.edu/~wpeng/Software.htm.
161
162 ------
163
164 .. class:: warningmark
165
166 By default, SICER creates files that do not conform to standards (e.g. BED files are closed, not half-open). This could have implications for downstream analysis.
167 To force the output of SICER to be formatted properly to standard file formats, check the **"Fix off-by-one errors in output files"** option.
168
169 ------
170
171 **Citation**
172
173 For the underlying tool, please cite `Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009 Aug 1;25(15):1952-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505939&gt;`_
174
175 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
176
177 </help>
178 </tool>