/tools/peak_calling/sicer_wrapper.xml
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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 155SICER 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 160View 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 173For 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>`_ 174 175If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* 176 177 </help> 178</tool>