Mercurial > repos > iuc > macs2
annotate macs2_callpeak.xml @ 4:56e104999978 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
| author | iuc |
|---|---|
| date | Mon, 06 Feb 2017 02:30:37 -0500 |
| parents | 6d4babad010f |
| children | beb902da6e5f |
| rev | line source |
|---|---|
| 0 | 1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.0"> |
| 2 <description>Call peaks from alignment results</description> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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3 <macros> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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4 <import>macs2_macros.xml</import> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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5 </macros> |
| 0 | 6 <expand macro="requirements"> |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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7 <requirement type="package" version="3.1.2">R</requirement> |
| 0 | 8 <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement> |
| 9 </expand> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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10 <expand macro="stdio" /> |
| 0 | 11 <expand macro="version_command" /> |
| 12 <command> | |
| 13 #set $temp_stderr = 'macs2_stderr' | |
| 14 (macs2 callpeak | |
| 15 | |
| 16 --name "MACS2" | |
| 17 -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_treatment_file ) ) } | |
| 18 | |
| 19 #if str( $input_control_file ) != 'None': | |
| 20 -c ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_control_file ) ) } | |
| 21 #end if | |
| 22 | |
| 23 #for $ifile in $input_treatment_file: | |
| 24 #if $ifile.ext.upper() == 'BAM' and $bampe: | |
| 25 --format BAMPE | |
| 26 #else | |
| 27 --format='$ifile.ext.upper()' | |
| 28 #end if | |
| 29 #end for | |
| 30 | |
| 31 @effective_genome_size@ | |
| 32 | |
| 33 --bw='$band_width' | |
| 34 | |
| 35 ## advanced options | |
| 36 #if $advanced_options.advanced_options_selector == 'on': | |
| 37 $advanced_options.nolambda | |
| 38 $advanced_options.to_large | |
| 39 --ratio $advanced_options.ratio | |
| 40 --slocal $advanced_options.slocal | |
| 41 --llocal $advanced_options.llocal | |
| 42 #if $advanced_options.broad_options.broad_options_selector == 'broad': | |
| 43 --broad | |
| 44 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }' | |
| 45 #else: | |
| 46 $advanced_options.broad_options.call_summits | |
| 47 #end if | |
| 48 | |
| 49 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user": | |
| 50 --keep-dup "${ advanced_options.keep_dup_options.user_keepdup }" | |
| 51 #else | |
| 52 --keep-dup "${ advanced_options.keep_dup_options.keep_dup_options_selector }" | |
| 53 #end if | |
| 54 | |
| 55 #end if | |
| 56 | |
| 57 ## With --bdg two additional output files will be generated. | |
| 58 #if 'bdg' in str($outputs).split(','): | |
| 59 --bdg | |
| 60 #end if | |
| 61 | |
| 62 ## cutoff selection | |
| 63 #if str( $cutoff_options.cutoff_options_selector ) == 'qvalue': | |
| 64 --qvalue "${ cutoff_options.qvalue }" | |
| 65 #elif str( $cutoff_options.cutoff_options_selector ) == 'pvalue': | |
| 66 #if str($cutoff_options.pvalue).strip() != '': | |
| 67 --pvalue "${ cutoff_options.pvalue }" | |
| 68 #end if | |
| 69 #end if | |
| 70 | |
| 71 ## model options | |
| 72 #if $nomodel_type.nomodel_type_selector == 'nomodel': | |
| 73 --nomodel | |
| 74 ##--shiftsize '$nomodel_type.shiftsize' | |
| 75 --extsize '${ nomodel_type.extsize }' | |
| 76 #end if | |
| 77 | |
| 78 2> $temp_stderr) | |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
2
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changeset
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79 #if 'peaks_tabular' in str($outputs).split(','): |
| 0 | 80 && |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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81 cp MACS2_peaks.xls "${ output_tabular }" |
| 0 | 82 #end if |
| 83 | |
| 84 ## run R to create pdf from model script | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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85 #if $nomodel_type.nomodel_type_selector == 'create_model' and 'pdf' in str($outputs).split(','): |
| 0 | 86 && |
| 87 Rscript MACS2_model.r > MACS2_model.r.log | |
| 88 #end if | |
| 89 | |
| 90 #if 'html' in str($outputs).split(','): | |
| 91 ## if output files exists, move them to the files_path and create a html result page linking to them | |
| 92 && | |
| 93 ( | |
| 94 count=`ls -1 MACS2* 2>/dev/null | wc -l`; | |
| 95 if [ \$count != 0 ]; | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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96 then |
| 0 | 97 mkdir "${ output_extra_files.files_path }"; |
| 98 cp MACS2* "${ output_extra_files.files_path }"; | |
| 99 python "\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.files_path }" $temp_stderr > "${ output_extra_files }"; | |
| 100 fi; | |
| 101 ) | |
| 102 #end if | |
| 103 ; | |
| 104 exit_code_for_galaxy=\$?; | |
| 105 cat $temp_stderr 2>&1; | |
| 106 (exit \$exit_code_for_galaxy) | |
| 107 </command> | |
| 108 <inputs> | |
| 109 <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="True" label="ChIP-Seq Treatment File" /> | |
| 110 <param name="input_control_file" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-Seq Control File" /> | |
| 111 | |
| 112 <param name="bampe" type="boolean" truevalue="--format BAMPE" falsevalue="" checked="False" label="Are your inputs Paired-end BAM files?" | |
| 113 help="The 'Build model step' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions. (--format BAMPE)"/> | |
| 114 | |
| 115 <expand macro="conditional_effective_genome_size" /> | |
| 116 <expand macro="band_width" /> | |
| 117 | |
| 118 <conditional name="cutoff_options"> | |
| 119 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value"> | |
| 120 <option value="qvalue" selected="true">q-value</option> | |
| 121 <option value="pvalue">p-value</option> | |
| 122 </param> | |
| 123 <when value="pvalue"> | |
| 124 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection" | |
| 125 help="default: not set (--pvalue)"/> | |
| 126 </when> | |
| 127 <when value="qvalue"> | |
| 128 <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection" | |
| 129 help="default: 0.05 (--qvalue)"/> | |
| 130 </when> | |
| 131 </conditional> | |
| 132 | |
| 133 <conditional name="nomodel_type"> | |
| 134 <param name="nomodel_type_selector" type="select" label="Build Model"> | |
| 135 <option value="nomodel">Do not build the shifting model (--nomodel)</option> | |
| 136 <option value="create_model" selected="true">Build the shifting model</option> | |
| 137 </param> | |
| 138 <when value="create_model"/> | |
| 139 <when value="nomodel"> | |
| 140 <!--<param name="shiftsize" type="integer" label="Arbitrary shift size in bp" value="100" help="(shiftsize)"/>--> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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141 <param name="extsize" type="integer" value="100" label="The arbitrary extension size in bp" |
| 0 | 142 help="MACS will use this value as fragment size to extend each read towards 3' end, then pile them up. It's exactly twice the number of legacy shiftsize. In previous language, each read is moved 3' direction to middle of fragment by 1/2 d, then extended to both direction with 1/2 d. This is equivalent to say each read is extended towards 3' into a d size fragment. DEFAULT: 200 (--extsize)"/> |
| 143 </when> | |
| 144 </conditional> | |
| 145 | |
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56e104999978
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
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146 <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" label="Outputs" help="PDF only created when model is build"> |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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147 <option value="peaks_tabular" selected="True">Peaks as tabular file</option> |
| 0 | 148 <!--<option value="narrow">narrow Peaks</option>--> |
| 149 <option value="summits" selected="true">summits</option> | |
| 150 <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option> | |
| 151 <option value="html">Summary page (html)</option> | |
| 152 <option value="pdf">Plot in PDF</option> | |
| 153 </param> | |
| 154 | |
| 155 <conditional name="advanced_options"> | |
| 156 <param name="advanced_options_selector" type="select" label="Advanced options"> | |
| 157 <option value="off" selected="true">Hide advanced options</option> | |
| 158 <option value="on">Display advanced options</option> | |
| 159 </param> | |
| 160 <when value="on"> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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161 <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" |
| 0 | 162 label="When set, scale the small sample up to the bigger sample" |
| 163 help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. (--to-large)"/> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
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diff
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164 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" |
| 0 | 165 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda)"/> |
| 166 <param name="ratio" type="float" value="1.0" | |
| 167 label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling" | |
| 168 help="(--ratio)"/> | |
| 169 <param name="slocal" value="1000" type="integer" label="The small nearby region in basepairs to calculate dynamic lambda" | |
| 170 help="This is used to capture the bias near the peak summit region. Invalid if there is no control data. If you set this to 0, MACS will skip slocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--slocal)"/> | |
| 171 <param name="llocal" value="10000" type="integer" label="The large nearby region in basepairs to calculate dynamic lambda" | |
| 172 help="This is used to capture the surround bias. If you set this to 0, MACS will skip llocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--llocal)"/> | |
| 173 <conditional name="broad_options"> | |
| 174 <param name="broad_options_selector" type="select" | |
| 175 label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)"> | |
| 176 <option value="nobroad" selected="true">No broad regions</option> | |
| 177 <option value="broad">broad regions</option> | |
| 178 </param> | |
| 179 <when value="broad"> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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180 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" |
| 0 | 181 help="value is either p-value or q-value as specified above (--broad-cutoff)"/> |
| 182 </when> | |
| 183 <when value="nobroad"> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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184 <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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185 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region" |
| 0 | 186 help="(--call-summits)"/> |
| 187 </when> | |
| 188 </conditional> | |
| 189 <expand macro="keep_duplicates" /> | |
| 190 </when> | |
| 191 <when value="off" /> | |
| 192 </conditional> | |
| 193 </inputs> | |
| 194 <outputs> | |
| 195 <!--callpeaks output--> | |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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196 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)"> |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
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197 <filter>'peaks_tabular' in outputs</filter> |
| 0 | 198 </data> |
| 199 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)"> | |
| 200 <filter> | |
| 201 (( | |
| 202 advanced_options['advanced_options_selector'] == "on" and | |
| 203 advanced_options['broad_options']['broad_options_selector'] == "broad" | |
| 204 )) | |
| 205 </filter> | |
| 206 </data> | |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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207 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> |
| 0 | 208 <filter> |
| 209 (( | |
| 210 advanced_options['advanced_options_selector'] == "on" and | |
| 211 advanced_options['broad_options']['broad_options_selector'] == "broad" | |
| 212 )) | |
| 213 </filter> | |
| 214 </data> | |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
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changeset
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215 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)"> |
| 0 | 216 <filter> |
| 217 ( | |
| 218 advanced_options['advanced_options_selector'] == "off" or | |
| 219 ( | |
| 220 advanced_options['advanced_options_selector'] == "on" and | |
| 221 advanced_options['broad_options']['broad_options_selector'] == "nobroad" | |
| 222 )) | |
| 223 </filter> | |
| 224 </data> | |
| 225 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)"> | |
| 226 <filter>'summits' in outputs</filter> | |
| 227 </data> | |
| 228 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)"> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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229 <filter> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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230 (( |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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231 'pdf' in outputs and |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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232 nomodel_type['nomodel_type_selector'] == "create_model" |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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233 )) |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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234 </filter> |
| 0 | 235 </data> |
| 236 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)"> | |
| 237 <filter>'bdg' in outputs</filter> | |
| 238 </data> | |
| 239 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)"> | |
| 240 <filter>'bdg' in outputs</filter> | |
| 241 </data> | |
| 242 <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)"> | |
| 243 <filter>'html' in outputs</filter> | |
| 244 </data> | |
| 245 </outputs> | |
| 246 <tests> | |
| 247 <test> | |
| 248 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> | |
| 249 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> | |
| 250 <param name="cutoff_options_selector" value="qvalue"/> | |
| 251 <param name="qvalue" value="0.05"/> | |
| 252 <param name="band_width" value="300"/> | |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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changeset
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253 <param name="outputs" value="peaks_tabular,bdg"/> |
| 0 | 254 <param name="effective_genome_size_options_selector" value="user_defined" /> |
| 255 <param name="gsize" value="3300000000" /> | |
| 256 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg"/> | |
| 257 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg"/> | |
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6d4babad010f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
2
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changeset
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258 <output name="output_tabular" compare="contains" file="callpeak_part.tabular"/> |
| 0 | 259 <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/> |
| 260 </test> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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261 <test> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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262 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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263 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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264 <param name="cutoff_options_selector" value="qvalue"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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265 <param name="qvalue" value="0.05"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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266 <param name="band_width" value="300"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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267 <param name="outputs" value="pdf"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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268 <param name="effective_genome_size_options_selector" value="user_defined" /> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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269 <param name="gsize" value="3300000000" /> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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270 <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" /> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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271 </test> |
| 0 | 272 </tests> |
| 273 <help> | |
| 274 **What it does** | |
| 275 | |
| 276 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) | |
| 277 is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for | |
| 278 identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of | |
| 279 binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. | |
| 280 | |
| 281 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README | |
| 282 | |
| 283 ------ | |
| 284 | |
| 285 **Usage** | |
| 286 | |
| 287 **Peak Calling**: Main MACS2 Function to Call peaks from alignment results. | |
| 288 | |
| 289 If you choose "Scores in bedGraph files" MACS will output the fragment pileup, control lambda, -log10-pvalue and -log10-qvalue scores in bedGraph files. | |
| 290 The peaks in BED format contain the following colomns: chr end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name | |
| 291 | |
| 292 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. | |
| 293 | |
| 294 | |
| 295 @citation@ | |
| 296 </help> | |
| 297 <expand macro="citations" /> | |
| 298 </tool> |