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comparison sicer_wrapper.xml @ 3:5c2cc3b58c7d draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
author devteam
date Wed, 28 Oct 2020 23:36:25 +0000
parents 74c9214cc8e6
children
comparison
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2:74c9214cc8e6 3:5c2cc3b58c7d
1 <tool id="peakcalling_sicer" name="SICER" version="0.0.2"> 1 <tool id="peakcalling_sicer" name="SICER" version="@TOOL_VERSION@">
2 <description>Statistical approach for the Identification of ChIP-Enriched Regions</description> 2 <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
3 <command interpreter="python">sicer_wrapper.py 3 <macros>
4 --bed_file '${input_bed_file}' 4 <token name="@TOOL_VERSION@">1.1</token>
5 #if str( $input_control_file ) != 'None': 5 </macros>
6 --control_file '${input_control_file}' 6 <requirements>
7 --significant_islands_output_file "${significant_islands_output_file}" 7 <requirement type="package" version="@TOOL_VERSION@">SICER</requirement>
8 --islands_summary_output_file "${islands_summary_output_file}" 8 </requirements>
9 --significant_islands_summary_output_file "${significant_islands_summary_output_file}" 9 <command detect_errors="exit_code"><![CDATA[
10 #end if 10 python '$__tool_directory__/sicer_wrapper.py'
11 ${fix_off_by_one_errors} 11 --bed_file '${input_bed_file}'
12 --dbkey '${input_bed_file.dbkey}' 12 #if str($input_control_file) != 'None':
13 --redundancy_threshold '${redundancy_threshold}' 13 --control_file '${input_control_file}'
14 --window_size '${window_size}' 14 --significant_islands_output_file "${significant_islands_output_file}"
15 --fragment_size '${fragment_size}' 15 --islands_summary_output_file "${islands_summary_output_file}"
16 --effective_genome_fraction '${effective_genome_fraction}' 16 --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
17 --gap_size '${gap_size}' 17 #end if
18 --error_cut_off '${error_cut_off}' 18 ${fix_off_by_one_errors}
19 ##output files 19 --dbkey '${input_bed_file.dbkey}'
20 --stdout "${output_log_file}" 20 --redundancy_threshold '${redundancy_threshold}'
21 --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}" 21 --window_size '${window_size}'
22 --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}" 22 --fragment_size '${fragment_size}'
23 --score_island_output_file "${score_island_output_file}" 23 --effective_genome_fraction '${effective_genome_fraction}'
24 --summary_graph_output_file "${summary_graph_output_file}" 24 --gap_size '${gap_size}'
25 --test_normalized_wig_output_file "${test_normalized_wig_output_file}" 25 --error_cut_off '${error_cut_off}'
26 --island_filtered_output_file "${island_filtered_output_file}" 26 ##output files
27 --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}" 27 --stdout "${output_log_file}"
28 </command> 28 --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
29 <requirements> 29 --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
30 <requirement type="package" version="1.1">SICER</requirement> 30 --score_island_output_file "${score_island_output_file}"
31 </requirements> 31 --summary_graph_output_file "${summary_graph_output_file}"
32 <inputs> 32 --test_normalized_wig_output_file "${test_normalized_wig_output_file}"
33 <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" > 33 --island_filtered_output_file "${island_filtered_output_file}"
34 <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator> 34 --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
35 </param> 35 ]]></command>
36 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys --> 36 <inputs>
37 <options> 37 <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
38 <filter type="data_meta" ref="input_bed_file" key="dbkey" /> 38 <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>
39 </options> 39 </param>
40 </param> 40 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="true"> <!-- fix me, add filter to match dbkeys -->
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"/> 41 <options>
42 <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" /> 42 <filter type="data_meta" ref="input_bed_file" key="dbkey" />
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" /> 43 </options>
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." /> 44 </param>
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." /> 45 <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"/>
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, ..." /> 46 <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
47 <param name="error_cut_off" type="float" label="Statistic threshold value" value="0.01" help="FDR (with control) or E-value (without control)" /> 47 <param name="window_size" type="integer" value="200" label="Window size" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
48 </inputs> 48 <param name="fragment_size" type="integer" value="150" label="Fragment size" 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." />
49 <outputs> 49 <param name="effective_genome_fraction" type="float" value="0.74" label="Effective genome fraction" help="Effective Genome as fraction of the genome size. It depends on read length." />
50 <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/> 50 <param name="gap_size" type="integer" value="600" label="Gap size" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
51 <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)"> 51 <param name="error_cut_off" type="float" value="0.01" label="Statistic threshold value" help="FDR (with control) or E-value (without control)" />
52 <filter>input_control_file is not None</filter> 52 </inputs>
53 </data> 53 <outputs>
54 <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/> 54 <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
55 <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/> 55 <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
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)"> 56 <filter>input_control_file is not None</filter>
57 <filter>input_control_file is not None</filter> 57 </data>
58 </data> 58 <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
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', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/> 59 <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
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', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/> 60 <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
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', $error_cut_off, '.scoreisland' ] ) ) #)"/> 61 <filter>input_control_file is not None</filter>
62 <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)"> 62 </data>
63 <filter>input_control_file is not None</filter> 63 <data name="island_filtered_output_file" format="bed" label="${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', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
64 </data> 64 <data name="island_filtered_normalized_wig_output_file" format="wig" label="${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', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
65 <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})"> 65 <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', $error_cut_off, '.scoreisland' ] ) ) #)"/>
66 <filter>input_control_file is not None</filter> 66 <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
67 </data> 67 <filter>input_control_file is not None</filter>
68 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> 68 </data>
69 </outputs> 69 <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
70 <tests> 70 <filter>input_control_file is not None</filter>
71 <test> 71 </data>
72 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> 72 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
73 <param name="input_control_file" /> 73 </outputs>
74 <param name="fix_off_by_one_errors" /> 74 <tests>
75 <param name="redundancy_threshold" value="1" /> 75 <test>
76 <param name="window_size" value="200" /> 76 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
77 <param name="fragment_size" value="150" /> 77 <param name="input_control_file" />
78 <param name="effective_genome_fraction" value="0.74" /> 78 <param name="fix_off_by_one_errors" />
79 <param name="gap_size" value="600" /> 79 <param name="redundancy_threshold" value="1" />
80 <param name="error_cut_off" value="0.01" /> 80 <param name="window_size" value="200" />
81 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" /> 81 <param name="fragment_size" value="150" />
82 <output name="summary_graph_output_file" file="test_1_test-W200.graph" /> 82 <param name="effective_genome_fraction" value="0.74" />
83 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" /> 83 <param name="gap_size" value="600" />
84 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" /> 84 <param name="error_cut_off" value="0.01" />
85 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" /> 85 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
86 <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" /> 86 <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
87 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/> 87 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
88 </test> 88 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
89 <test> 89 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
90 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> 90 <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />
91 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" /> 91 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
92 <param name="fix_off_by_one_errors" /> 92 </test>
93 <param name="redundancy_threshold" value="1" /> 93 <test>
94 <param name="window_size" value="200" /> 94 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
95 <param name="fragment_size" value="150" /> 95 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
96 <param name="effective_genome_fraction" value="0.74" /> 96 <param name="fix_off_by_one_errors" />
97 <param name="gap_size" value="600" /> 97 <param name="redundancy_threshold" value="1" />
98 <param name="error_cut_off" value="0.01" /> 98 <param name="window_size" value="200" />
99 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" /> 99 <param name="fragment_size" value="150" />
100 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" /> 100 <param name="effective_genome_fraction" value="0.74" />
101 <output name="summary_graph_output_file" file="test_1_test-W200.graph" /> 101 <param name="gap_size" value="600" />
102 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" /> 102 <param name="error_cut_off" value="0.01" />
103 <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" /> 103 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
104 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" /> 104 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
105 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" /> 105 <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
106 <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" /> 106 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
107 <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" /> 107 <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" />
108 <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" /> 108 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
109 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/> 109 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
110 </test> 110 <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" />
111 <test> 111 <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" />
112 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> 112 <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" />
113 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" /> 113 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
114 <param name="fix_off_by_one_errors" value="True" /> 114 </test>
115 <param name="redundancy_threshold" value="1" /> 115 <test>
116 <param name="window_size" value="200" /> 116 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
117 <param name="fragment_size" value="150" /> 117 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
118 <param name="effective_genome_fraction" value="0.74" /> 118 <param name="fix_off_by_one_errors" value="True" />
119 <param name="gap_size" value="600" /> 119 <param name="redundancy_threshold" value="1" />
120 <param name="error_cut_off" value="0.01" /> 120 <param name="window_size" value="200" />
121 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" /> 121 <param name="fragment_size" value="150" />
122 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" /> 122 <param name="effective_genome_fraction" value="0.74" />
123 <output name="summary_graph_output_file" file="test_3_test-W200.graph" /> 123 <param name="gap_size" value="600" />
124 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" /> 124 <param name="error_cut_off" value="0.01" />
125 <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" /> 125 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
126 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" /> 126 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
127 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" /> 127 <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
128 <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" /> 128 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
129 <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" /> 129 <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />
130 <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" /> 130 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
131 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/> 131 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
132 </test> 132 <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />
133 <test> 133 <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />
134 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> 134 <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />
135 <param name="input_control_file" /> 135 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
136 <param name="fix_off_by_one_errors" value="True" /> 136 </test>
137 <param name="redundancy_threshold" value="1" /> 137 <test>
138 <param name="window_size" value="200" /> 138 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
139 <param name="fragment_size" value="150" /> 139 <param name="input_control_file" />
140 <param name="effective_genome_fraction" value="0.74" /> 140 <param name="fix_off_by_one_errors" value="True" />
141 <param name="gap_size" value="600" /> 141 <param name="redundancy_threshold" value="1" />
142 <param name="error_cut_off" value="0.01" /> 142 <param name="window_size" value="200" />
143 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" /> 143 <param name="fragment_size" value="150" />
144 <output name="summary_graph_output_file" file="test_3_test-W200.graph" /> 144 <param name="effective_genome_fraction" value="0.74" />
145 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" /> 145 <param name="gap_size" value="600" />
146 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" /> 146 <param name="error_cut_off" value="0.01" />
147 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" /> 147 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
148 <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" /> 148 <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
149 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/> 149 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
150 </test> 150 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
151 </tests> 151 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
152 <help> 152 <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />
153 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
154 </test>
155 </tests>
156 <help><![CDATA[
153 **What it does** 157 **What it does**
154 158
155 SICER first and foremost is a filtering tool. Its main functions are:: 159 SICER first and foremost is a filtering tool. Its main functions are::
156 160
157 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks. 161 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks.
168 172
169 ------ 173 ------
170 174
171 **Citation** 175 **Citation**
172 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* 176 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
173 177 ]]></help>
174 </help> 178 <citations>
175 <citations> 179 <citation type="doi">10.1093/bioinformatics/btp340</citation>
176 <citation type="doi">10.1093/bioinformatics/btp340</citation> 180 </citations>
177 </citations>
178 </tool> 181 </tool>