macs2: macs2_callpeak.xml annotate

annotate macs2_callpeak.xml @ 51:61d2f23acfb8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681

author	iuc
date	Wed, 12 Apr 2017 01:47:11 -0400
parents	332bb7b61205
children	6c9ea5f92ddb

rev	line source
33 c82a1f154c60 Uploaded iuc parents: diff changeset	1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.0">
c82a1f154c60 Uploaded iuc parents: diff changeset	2 <description>Call peaks from alignment results</description>
36 8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	3 <macros>
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	4 <import>macs2_macros.xml</import>
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	5 </macros>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	6 <expand macro="requirements">
c82a1f154c60 Uploaded iuc parents: diff changeset	7 </expand>
36 8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	8 <expand macro="stdio" />
33 c82a1f154c60 Uploaded iuc parents: diff changeset	9 <expand macro="version_command" />
c82a1f154c60 Uploaded iuc parents: diff changeset	10 <command>
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	11 <![CDATA[
33 c82a1f154c60 Uploaded iuc parents: diff changeset	12 #set $temp_stderr = 'macs2_stderr'
c82a1f154c60 Uploaded iuc parents: diff changeset	13 (macs2 callpeak
c82a1f154c60 Uploaded iuc parents: diff changeset	14
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	15 --name 'MACS2'
33 c82a1f154c60 Uploaded iuc parents: diff changeset	16 -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_treatment_file ) ) }
c82a1f154c60 Uploaded iuc parents: diff changeset	17
c82a1f154c60 Uploaded iuc parents: diff changeset	18 #if str( $input_control_file ) != 'None':
c82a1f154c60 Uploaded iuc parents: diff changeset	19 -c ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_control_file ) ) }
c82a1f154c60 Uploaded iuc parents: diff changeset	20 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	21
c82a1f154c60 Uploaded iuc parents: diff changeset	22 #for $ifile in $input_treatment_file:
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	23 #if $ifile.ext.upper() == "BAM" and $bampe:
33 c82a1f154c60 Uploaded iuc parents: diff changeset	24 --format BAMPE
c82a1f154c60 Uploaded iuc parents: diff changeset	25 #else
c82a1f154c60 Uploaded iuc parents: diff changeset	26 --format='$ifile.ext.upper()'
c82a1f154c60 Uploaded iuc parents: diff changeset	27 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	28 #end for
c82a1f154c60 Uploaded iuc parents: diff changeset	29
c82a1f154c60 Uploaded iuc parents: diff changeset	30 @effective_genome_size@
c82a1f154c60 Uploaded iuc parents: diff changeset	31
51 61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	32 --bw '${band_width}'
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	33 @mfold_command@
33 c82a1f154c60 Uploaded iuc parents: diff changeset	34
c82a1f154c60 Uploaded iuc parents: diff changeset	35 ## advanced options
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	36 #if $advanced_options.advanced_options_selector == "on":
33 c82a1f154c60 Uploaded iuc parents: diff changeset	37 $advanced_options.nolambda
c82a1f154c60 Uploaded iuc parents: diff changeset	38 $advanced_options.to_large
c82a1f154c60 Uploaded iuc parents: diff changeset	39 --ratio $advanced_options.ratio
c82a1f154c60 Uploaded iuc parents: diff changeset	40 --slocal $advanced_options.slocal
c82a1f154c60 Uploaded iuc parents: diff changeset	41 --llocal $advanced_options.llocal
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	42 #if $advanced_options.broad_options.broad_options_selector == "broad":
33 c82a1f154c60 Uploaded iuc parents: diff changeset	43 --broad
c82a1f154c60 Uploaded iuc parents: diff changeset	44 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
c82a1f154c60 Uploaded iuc parents: diff changeset	45 #else:
c82a1f154c60 Uploaded iuc parents: diff changeset	46 $advanced_options.broad_options.call_summits
c82a1f154c60 Uploaded iuc parents: diff changeset	47 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	48
c82a1f154c60 Uploaded iuc parents: diff changeset	49 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	50 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
33 c82a1f154c60 Uploaded iuc parents: diff changeset	51 #else
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	52 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
33 c82a1f154c60 Uploaded iuc parents: diff changeset	53 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	54
c82a1f154c60 Uploaded iuc parents: diff changeset	55 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	56
c82a1f154c60 Uploaded iuc parents: diff changeset	57 ## With --bdg two additional output files will be generated.
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	58 #if "bdg" in str($outputs).split(','):
33 c82a1f154c60 Uploaded iuc parents: diff changeset	59 --bdg
c82a1f154c60 Uploaded iuc parents: diff changeset	60 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	61
c82a1f154c60 Uploaded iuc parents: diff changeset	62 ## cutoff selection
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	63 #if str( $cutoff_options.cutoff_options_selector ) == "qvalue":
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	64 --qvalue '${ cutoff_options.qvalue }'
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	65 #elif str( $cutoff_options.cutoff_options_selector ) == "pvalue":
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	66 #if str($cutoff_options.pvalue).strip() != "":
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	67 --pvalue '${ cutoff_options.pvalue }'
33 c82a1f154c60 Uploaded iuc parents: diff changeset	68 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	69 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	70
c82a1f154c60 Uploaded iuc parents: diff changeset	71 ## model options
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	72 #if $nomodel_type.nomodel_type_selector == "nomodel":
33 c82a1f154c60 Uploaded iuc parents: diff changeset	73 --nomodel
c82a1f154c60 Uploaded iuc parents: diff changeset	74 --extsize '${ nomodel_type.extsize }'
c82a1f154c60 Uploaded iuc parents: diff changeset	75 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	76
51 61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	77 2>&1 > $temp_stderr)
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	78 #if "peaks_tabular" in str($outputs).split(','):
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	79 &&
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	80 cp MACS2_peaks.xls '${ output_tabular }'
33 c82a1f154c60 Uploaded iuc parents: diff changeset	81 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	82
c82a1f154c60 Uploaded iuc parents: diff changeset	83 ## run R to create pdf from model script
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	84 #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(','):
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	85 &&
33 c82a1f154c60 Uploaded iuc parents: diff changeset	86 Rscript MACS2_model.r > MACS2_model.r.log
c82a1f154c60 Uploaded iuc parents: diff changeset	87 #end if
c82a1f154c60 Uploaded iuc parents: diff changeset	88
c82a1f154c60 Uploaded iuc parents: diff changeset	89 #if 'html' in str($outputs).split(','):
c82a1f154c60 Uploaded iuc parents: diff changeset	90 ## if output files exists, move them to the files_path and create a html result page linking to them
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	91 &&
33 c82a1f154c60 Uploaded iuc parents: diff changeset	92 (
c82a1f154c60 Uploaded iuc parents: diff changeset	93 count=`ls -1 MACS2* 2>/dev/null \| wc -l`;
c82a1f154c60 Uploaded iuc parents: diff changeset	94 if [ \$count != 0 ];
36 8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	95 then
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	96 mkdir '${ output_extra_files.files_path }' &&
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	97 cp MACS2* '${ output_extra_files.files_path }' &&
51 61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	98 python '$__tool_directory__/dir2html.py'
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	99 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }';
33 c82a1f154c60 Uploaded iuc parents: diff changeset	100 fi;
c82a1f154c60 Uploaded iuc parents: diff changeset	101 )
c82a1f154c60 Uploaded iuc parents: diff changeset	102 #end if
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	103 &&
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	104 exit_code_for_galaxy=\$? &&
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	105 cat $temp_stderr 2>&1 &&
33 c82a1f154c60 Uploaded iuc parents: diff changeset	106 (exit \$exit_code_for_galaxy)
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	107 ]]>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	108 </command>
c82a1f154c60 Uploaded iuc parents: diff changeset	109 <inputs>
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	110 <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="true"
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	111 label="ChIP-Seq Treatment File" />
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	112 <param name="input_control_file" type="data" format="bam,sam,bed" multiple="true" optional="True"
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	113 label="ChIP-Seq Control File" />
33 c82a1f154c60 Uploaded iuc parents: diff changeset	114
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	115 <param name="bampe" type="boolean" truevalue="--format BAMPE" falsevalue="" checked="False"
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	116 label="Are your inputs Paired-end BAM files?"
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	117 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)"/>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	118
c82a1f154c60 Uploaded iuc parents: diff changeset	119 <expand macro="conditional_effective_genome_size" />
c82a1f154c60 Uploaded iuc parents: diff changeset	120 <expand macro="band_width" />
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	121 <expand macro="mfold_options" />
33 c82a1f154c60 Uploaded iuc parents: diff changeset	122
c82a1f154c60 Uploaded iuc parents: diff changeset	123 <conditional name="cutoff_options">
c82a1f154c60 Uploaded iuc parents: diff changeset	124 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
c82a1f154c60 Uploaded iuc parents: diff changeset	125 <option value="qvalue" selected="true">q-value</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	126 <option value="pvalue">p-value</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	127 </param>
c82a1f154c60 Uploaded iuc parents: diff changeset	128 <when value="pvalue">
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	129 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection" help="default: not set (--pvalue)"/>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	130 </when>
c82a1f154c60 Uploaded iuc parents: diff changeset	131 <when value="qvalue">
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	132 <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection" help="The q-value (minimum FDR) cutoff to call significant regions. Default is 0.01. For broad marks, you can try 0.05 as cutoff. Q-values are calculated from p-values using Benjamini-Hochberg procedure. (--qvalue)"/>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	133 </when>
c82a1f154c60 Uploaded iuc parents: diff changeset	134 </conditional>
c82a1f154c60 Uploaded iuc parents: diff changeset	135
c82a1f154c60 Uploaded iuc parents: diff changeset	136 <conditional name="nomodel_type">
c82a1f154c60 Uploaded iuc parents: diff changeset	137 <param name="nomodel_type_selector" type="select" label="Build Model">
c82a1f154c60 Uploaded iuc parents: diff changeset	138 <option value="nomodel">Do not build the shifting model (--nomodel)</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	139 <option value="create_model" selected="true">Build the shifting model</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	140 </param>
c82a1f154c60 Uploaded iuc parents: diff changeset	141 <when value="create_model"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	142 <when value="nomodel">
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	143 <param name="extsize" type="integer" value="200" label="Set extension size" help="The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3-prime; end, then pile them up. It is exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5-prime-to-3-prime direction to middle of fragment by 0.5 d, then extended to both direction with 0.5 d. This is equivalent to say each read is extended towards 5-prime-to-3-prime into a d size fragment. --extsize (this option) and --shift (the option below) can be combined when necessary. See --shift option below. Default = 200 (--extsize)."/>
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	144 <param name="shift" type="integer" value="0" label="Set shift size" help="(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5-prime) towards 5-prime-to-3-prime direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3-prime-to-5-prime direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * 0.5 of --extsize (option above) together with --extsize option for detecting enriched cutting loci such as certain DNAseI-Seq datasets. Note, you can't set values other than 0 if format is BAMPE for paired-end data. Default = 0 (--shift)."/>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	145 </when>
c82a1f154c60 Uploaded iuc parents: diff changeset	146 </conditional>
c82a1f154c60 Uploaded iuc parents: diff changeset	147
48 e04fc51ee5e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 47 diff changeset	148 <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" label="Outputs" help="PDF only created when model is build">
47 9033b59bf9c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 44 diff changeset	149 <option value="peaks_tabular" selected="True">Peaks as tabular file</option>
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	150 <option value="summits" selected="true">Peak summits</option>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	151 <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	152 <option value="html">Summary page (html)</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	153 <option value="pdf">Plot in PDF</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	154 </param>
c82a1f154c60 Uploaded iuc parents: diff changeset	155
c82a1f154c60 Uploaded iuc parents: diff changeset	156 <conditional name="advanced_options">
c82a1f154c60 Uploaded iuc parents: diff changeset	157 <param name="advanced_options_selector" type="select" label="Advanced options">
c82a1f154c60 Uploaded iuc parents: diff changeset	158 <option value="off" selected="true">Hide advanced options</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	159 <option value="on">Display advanced options</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	160 </param>
c82a1f154c60 Uploaded iuc parents: diff changeset	161 <when value="on">
36 8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	162 <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False"
33 c82a1f154c60 Uploaded iuc parents: diff changeset	163 label="When set, scale the small sample up to the bigger sample"
c82a1f154c60 Uploaded iuc parents: diff changeset	164 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)"/>
36 8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	165 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False"
33 c82a1f154c60 Uploaded iuc parents: diff changeset	166 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda)"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	167 <param name="ratio" type="float" value="1.0"
c82a1f154c60 Uploaded iuc parents: diff changeset	168 label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
c82a1f154c60 Uploaded iuc parents: diff changeset	169 help="(--ratio)"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	170 <param name="slocal" value="1000" type="integer" label="The small nearby region in basepairs to calculate dynamic lambda"
c82a1f154c60 Uploaded iuc parents: diff changeset	171 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)"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	172 <param name="llocal" value="10000" type="integer" label="The large nearby region in basepairs to calculate dynamic lambda"
c82a1f154c60 Uploaded iuc parents: diff changeset	173 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)"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	174 <conditional name="broad_options">
c82a1f154c60 Uploaded iuc parents: diff changeset	175 <param name="broad_options_selector" type="select"
c82a1f154c60 Uploaded iuc parents: diff changeset	176 label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)">
c82a1f154c60 Uploaded iuc parents: diff changeset	177 <option value="nobroad" selected="true">No broad regions</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	178 <option value="broad">broad regions</option>
c82a1f154c60 Uploaded iuc parents: diff changeset	179 </param>
c82a1f154c60 Uploaded iuc parents: diff changeset	180 <when value="broad">
36 8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	181 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
33 c82a1f154c60 Uploaded iuc parents: diff changeset	182 help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	183 </when>
c82a1f154c60 Uploaded iuc parents: diff changeset	184 <when value="nobroad">
36 8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	185 <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 33 diff changeset	186 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"
33 c82a1f154c60 Uploaded iuc parents: diff changeset	187 help="(--call-summits)"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	188 </when>
c82a1f154c60 Uploaded iuc parents: diff changeset	189 </conditional>
c82a1f154c60 Uploaded iuc parents: diff changeset	190 <expand macro="keep_duplicates" />
c82a1f154c60 Uploaded iuc parents: diff changeset	191 </when>
c82a1f154c60 Uploaded iuc parents: diff changeset	192 <when value="off" />
c82a1f154c60 Uploaded iuc parents: diff changeset	193 </conditional>
c82a1f154c60 Uploaded iuc parents: diff changeset	194 </inputs>
c82a1f154c60 Uploaded iuc parents: diff changeset	195 <outputs>
c82a1f154c60 Uploaded iuc parents: diff changeset	196 <!--callpeaks output-->
47 9033b59bf9c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 44 diff changeset	197 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)">
9033b59bf9c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 44 diff changeset	198 <filter>'peaks_tabular' in outputs</filter>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	199 </data>
c82a1f154c60 Uploaded iuc parents: diff changeset	200 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
c82a1f154c60 Uploaded iuc parents: diff changeset	201 <filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	202 ((
c82a1f154c60 Uploaded iuc parents: diff changeset	203 advanced_options['advanced_options_selector'] == "on" and
c82a1f154c60 Uploaded iuc parents: diff changeset	204 advanced_options['broad_options']['broad_options_selector'] == "broad"
c82a1f154c60 Uploaded iuc parents: diff changeset	205 ))
c82a1f154c60 Uploaded iuc parents: diff changeset	206 </filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	207 </data>
47 9033b59bf9c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 44 diff changeset	208 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
33 c82a1f154c60 Uploaded iuc parents: diff changeset	209 <filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	210 ((
c82a1f154c60 Uploaded iuc parents: diff changeset	211 advanced_options['advanced_options_selector'] == "on" and
c82a1f154c60 Uploaded iuc parents: diff changeset	212 advanced_options['broad_options']['broad_options_selector'] == "broad"
c82a1f154c60 Uploaded iuc parents: diff changeset	213 ))
c82a1f154c60 Uploaded iuc parents: diff changeset	214 </filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	215 </data>
47 9033b59bf9c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 44 diff changeset	216 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
33 c82a1f154c60 Uploaded iuc parents: diff changeset	217 <filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	218 (
c82a1f154c60 Uploaded iuc parents: diff changeset	219 advanced_options['advanced_options_selector'] == "off" or
c82a1f154c60 Uploaded iuc parents: diff changeset	220 (
c82a1f154c60 Uploaded iuc parents: diff changeset	221 advanced_options['advanced_options_selector'] == "on" and
c82a1f154c60 Uploaded iuc parents: diff changeset	222 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
c82a1f154c60 Uploaded iuc parents: diff changeset	223 ))
c82a1f154c60 Uploaded iuc parents: diff changeset	224 </filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	225 </data>
c82a1f154c60 Uploaded iuc parents: diff changeset	226 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">
c82a1f154c60 Uploaded iuc parents: diff changeset	227 <filter>'summits' in outputs</filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	228 </data>
c82a1f154c60 Uploaded iuc parents: diff changeset	229 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
44 37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	230 <filter>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	231 ((
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	232 'pdf' in outputs and
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	233 nomodel_type['nomodel_type_selector'] == "create_model"
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	234 ))
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	235 </filter>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	236 </data>
c82a1f154c60 Uploaded iuc parents: diff changeset	237 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
c82a1f154c60 Uploaded iuc parents: diff changeset	238 <filter>'bdg' in outputs</filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	239 </data>
c82a1f154c60 Uploaded iuc parents: diff changeset	240 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)">
c82a1f154c60 Uploaded iuc parents: diff changeset	241 <filter>'bdg' in outputs</filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	242 </data>
c82a1f154c60 Uploaded iuc parents: diff changeset	243 <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)">
c82a1f154c60 Uploaded iuc parents: diff changeset	244 <filter>'html' in outputs</filter>
c82a1f154c60 Uploaded iuc parents: diff changeset	245 </data>
c82a1f154c60 Uploaded iuc parents: diff changeset	246 </outputs>
c82a1f154c60 Uploaded iuc parents: diff changeset	247 <tests>
c82a1f154c60 Uploaded iuc parents: diff changeset	248 <test>
c82a1f154c60 Uploaded iuc parents: diff changeset	249 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	250 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	251 <param name="cutoff_options_selector" value="qvalue"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	252 <param name="qvalue" value="0.05"/>
c82a1f154c60 Uploaded iuc parents: diff changeset	253 <param name="band_width" value="300"/>
51 61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	254 <param name="outputs" value="peaks_tabular,bdg,html"/>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	255 <param name="effective_genome_size_options_selector" value="user_defined" />
c82a1f154c60 Uploaded iuc parents: diff changeset	256 <param name="gsize" value="3300000000" />
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	257 <param name="lower" value="5" />
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	258 <param name="upper" value="50" />
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	259 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	260 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	261 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/>
51 61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	262 <output name="output_extra_files">
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	263 <assert_contents>
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	264 <has_text text="Additional output created by MACS2" />
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	265 </assert_contents>
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	266 </output>
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 iuc parents: 50 diff changeset	267
33 c82a1f154c60 Uploaded iuc parents: diff changeset	268 </test>
44 37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	269 <test>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	270 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	271 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	272 <param name="cutoff_options_selector" value="qvalue"/>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	273 <param name="qvalue" value="0.05"/>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	274 <param name="band_width" value="300"/>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	275 <param name="outputs" value="pdf"/>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	276 <param name="effective_genome_size_options_selector" value="user_defined" />
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	277 <param name="gsize" value="3300000000" />
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	278 <param name="lower" value="5" />
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	279 <param name="upper" value="50" />
44 37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	280 <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" />
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74 iuc parents: 36 diff changeset	281 </test>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	282 </tests>
c82a1f154c60 Uploaded iuc parents: diff changeset	283 <help>
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	284 <![CDATA[
33 c82a1f154c60 Uploaded iuc parents: diff changeset	285 What it does
c82a1f154c60 Uploaded iuc parents: diff changeset	286
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	287 callpeak is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments.
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	288 It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions,
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	289 and improves the spatial resolution of binding sites through combining the information of both sequencing
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	290 tag position and orientation. MACS can be used for ChIP-Seq data alone, or with control sample with the
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	291 increase of specificity (recommended).
33 c82a1f154c60 Uploaded iuc parents: diff changeset	292
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	293 .. _MACS2: https://github.com/taoliu/MACS
33 c82a1f154c60 Uploaded iuc parents: diff changeset	294
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	295 MACS2 performs the following analysis steps:
33 c82a1f154c60 Uploaded iuc parents: diff changeset	296
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	297 * Artificially extend reads to expected fragment length, and generate coverage map along genome.
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	298 * Assume background reads are Poisson distributed. Mean of the Poisson is locally variable and is estimated from control experiment (if available) in 5Kbp or 10Kbp around examined location.
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	299 * For a given location, do we see more reads than we would have expected from the Poisson (p < 0.00005)? If Yes, MACS2 calls a peak.
33 c82a1f154c60 Uploaded iuc parents: diff changeset	300
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	301
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	302 .. class:: warningmark
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	303
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	304 If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend mfold range by increasing the upper bound or play with Build model options.
33 c82a1f154c60 Uploaded iuc parents: diff changeset	305
c82a1f154c60 Uploaded iuc parents: diff changeset	306
c82a1f154c60 Uploaded iuc parents: diff changeset	307 @citation@
49 1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b iuc parents: 48 diff changeset	308 ]]>
33 c82a1f154c60 Uploaded iuc parents: diff changeset	309 </help>
c82a1f154c60 Uploaded iuc parents: diff changeset	310 <expand macro="citations" />
c82a1f154c60 Uploaded iuc parents: diff changeset	311 </tool>

Mercurial > repos > iuc > macs2

annotate macs2_callpeak.xml @ 51:61d2f23acfb8 draft