Mercurial > repos > devteam > sicer
annotate sicer_wrapper.xml @ 1:4a14714649b4 draft
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Tue, 21 Jul 2015 15:59:56 -0400 |
| parents | 82a8234e03f2 |
| children | 74c9214cc8e6 |
| rev | line source |
|---|---|
| 0 | 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 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* | |
| 173 | |
| 174 </help> | |
|
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175 <citations> |
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planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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176 <citation type="doi">10.1093/bioinformatics/btp340</citation> |
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planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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177 </citations> |
| 0 | 178 </tool> |