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1 <tool id="peakcalling_sicer" name="SICER" version="0.0.1">
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2 <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
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3 <command interpreter="python">sicer_wrapper.py
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4 --bed_file '${input_bed_file}'
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5 #if str( $input_control_file ) != 'None':
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6 --control_file '${input_control_file}'
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7 --significant_islands_output_file "${significant_islands_output_file}"
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8 --islands_summary_output_file "${islands_summary_output_file}"
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9 --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
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10 #end if
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11 ${fix_off_by_one_errors}
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12 --dbkey '${input_bed_file.dbkey}'
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13 --redundancy_threshold '${redundancy_threshold}'
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14 --window_size '${window_size}'
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15 --fragment_size '${fragment_size}'
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16 --effective_genome_fraction '${effective_genome_fraction}'
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17 --gap_size '${gap_size}'
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18 --error_cut_off '${error_cut_off}'
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19 ##output files
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20 --stdout "${output_log_file}"
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21 --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
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22 --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
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23 --score_island_output_file "${score_island_output_file}"
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24 --summary_graph_output_file "${summary_graph_output_file}"
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25 --test_normalized_wig_output_file "${test_normalized_wig_output_file}"
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26 --island_filtered_output_file "${island_filtered_output_file}"
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27 --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
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28 </command>
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29 <requirements>
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30 <requirement type="package" version="1.1">SICER</requirement>
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31 </requirements>
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32 <inputs>
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33 <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
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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>
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35 </param>
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36 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys -->
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37 <options>
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38 <filter type="data_meta" ref="input_bed_file" key="dbkey" />
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39 </options>
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40 </param>
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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"/>
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42 <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
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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" />
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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." />
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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." />
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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, ..." />
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47 <param name="error_cut_off" type="float" label="Statistic threshold value" value="0.01" help="FDR (with control) or E-value (without control)" />
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48 </inputs>
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49 <outputs>
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50 <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
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51 <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
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52 <filter>input_control_file is not None</filter>
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53 </data>
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54 <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
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55 <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
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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)">
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57 <filter>input_control_file is not None</filter>
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58 </data>
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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', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
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60 <data name="island_filtered_normalized_wig_output_file" format="wig" label="${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', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
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61 <data name="score_island_output_file" format="interval" label="${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', $error_cut_off, '.scoreisland' ] ) ) #)"/>
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62 <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
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63 <filter>input_control_file is not None</filter>
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64 </data>
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65 <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
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66 <filter>input_control_file is not None</filter>
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67 </data>
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68 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
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73 <param name="input_control_file" />
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74 <param name="fix_off_by_one_errors" />
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75 <param name="redundancy_threshold" value="1" />
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76 <param name="window_size" value="200" />
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77 <param name="fragment_size" value="150" />
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78 <param name="effective_genome_fraction" value="0.74" />
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79 <param name="gap_size" value="600" />
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80 <param name="error_cut_off" value="0.01" />
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81 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />
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82 <output name="summary_graph_output_file" file="peakcalling_sicer/test_1/test-W200.graph" />
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83 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />
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84 <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />
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85 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />
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86 <output name="score_island_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland" />
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87 <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>
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88 </test>
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89 <test>
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90 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
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91 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
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92 <param name="fix_off_by_one_errors" />
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93 <param name="redundancy_threshold" value="1" />
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94 <param name="window_size" value="200" />
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95 <param name="fragment_size" value="150" />
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96 <param name="effective_genome_fraction" value="0.74" />
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97 <param name="gap_size" value="600" />
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98 <param name="error_cut_off" value="0.01" />
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99 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />
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100 <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />
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101 <output name="summary_graph_output_file" file="peakcalling_sicer/test_2/test-W200.graph" />
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102 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />
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103 <output name="significant_islands_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed" />
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104 <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />
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105 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
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106 <output name="score_island_output_file" file="peakcalling_sicer/test_2/test-W200-G600.scoreisland" />
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107 <output name="islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary" />
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108 <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01" />
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109 <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>
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110 </test>
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111 <test>
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112 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
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113 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
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114 <param name="fix_off_by_one_errors" value="True" />
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115 <param name="redundancy_threshold" value="1" />
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116 <param name="window_size" value="200" />
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117 <param name="fragment_size" value="150" />
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118 <param name="effective_genome_fraction" value="0.74" />
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119 <param name="gap_size" value="600" />
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120 <param name="error_cut_off" value="0.01" />
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121 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" />
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122 <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" />
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123 <output name="summary_graph_output_file" file="peakcalling_sicer/test_3/test-W200.graph" />
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124 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" />
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125 <output name="significant_islands_output_file" file="peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed" />
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126 <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" />
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127 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
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128 <output name="score_island_output_file" file="peakcalling_sicer/test_3/test-W200-G600.scoreisland" />
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129 <output name="islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary" />
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130 <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01" />
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131 <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/>
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132 </test>
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133 <test>
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134 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
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135 <param name="input_control_file" />
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136 <param name="fix_off_by_one_errors" value="True" />
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137 <param name="redundancy_threshold" value="1" />
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138 <param name="window_size" value="200" />
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139 <param name="fragment_size" value="150" />
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140 <param name="effective_genome_fraction" value="0.74" />
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141 <param name="gap_size" value="600" />
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142 <param name="error_cut_off" value="0.01" />
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143 <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" />
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144 <output name="summary_graph_output_file" file="peakcalling_sicer/test_4/test-W200.graph" />
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145 <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" />
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146 <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" />
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147 <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" />
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148 <output name="score_island_output_file" file="peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland" />
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149 <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/>
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150 </test>
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151 </tests>
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152 <help>
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153 **What it does**
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154
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155 SICER first and foremost is a filtering tool. Its main functions are::
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156
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157 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks.
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158 2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.
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159
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160 View the original SICER documentation: http://home.gwu.edu/~wpeng/Software.htm.
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161
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162 ------
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163
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164 .. class:: warningmark
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165
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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.
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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.
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168
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169 ------
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170
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171 **Citation**
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172
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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. <http://www.ncbi.nlm.nih.gov/pubmed/19505939>`_
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174
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175 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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176
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177 </help>
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178 </tool>
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