Mercurial > repos > iuc > macs2
annotate macs2_callpeak.xml @ 8:e8a060164e11 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
author | iuc |
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date | Wed, 27 Dec 2017 10:18:03 -0500 |
parents | f5d67c722d67 |
children | acbd3fb47f90 |
rev | line source |
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8
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.1"> |
0 | 2 <description>Call peaks from alignment results</description> |
2
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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3 <macros> |
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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4 <import>macs2_macros.xml</import> |
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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5 </macros> |
0 | 6 <expand macro="requirements"> |
7 </expand> | |
2
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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changeset
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8 <expand macro="stdio" /> |
0 | 9 <expand macro="version_command" /> |
8
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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10 <command><![CDATA[ |
0 | 11 #set $temp_stderr = 'macs2_stderr' |
12 (macs2 callpeak | |
13 | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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14 --name 'MACS2' |
8
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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changeset
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15 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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16 ## Treatment File(s) |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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17 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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changeset
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18 #if str($treatment.t_multi_select) == "Yes": |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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19 -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), '$treatment.input_treatment_file' ) ) } |
0 | 20 |
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e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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21 #if '$treatment.input_treatment_file[0].ext.upper()' == "BAM" and $bampe: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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22 --format BAMPE |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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changeset
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23 #else |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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24 --format='$treatment.input_treatment_file[0].ext.upper()' |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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changeset
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25 #end if |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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diff
changeset
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26 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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changeset
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27 #else |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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changeset
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28 -t '$treatment.input_treatment_file' |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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29 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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diff
changeset
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30 #if '$treatment.input_treatment_file.ext.upper()' == "BAM" and $bampe: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
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31 --format BAMPE |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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changeset
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32 #else |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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changeset
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33 --format='$treatment.input_treatment_file.ext.upper()' |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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34 #end if |
0 | 35 #end if |
36 | |
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e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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changeset
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37 ## Control File(s) |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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38 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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39 #if str($control.c_select) == "Yes": |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
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40 #if str($control.c_multiple.c_multi_select) == "Yes": |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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41 -c ${ ' '.join( map( lambda x:'"%s"' % ( x ), '$control.c_multiple.input_control_file' ) ) } |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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changeset
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42 #else |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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43 -c '$control.c_multiple.input_control_file' |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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44 #end if |
0 | 45 #end if |
46 | |
47 @effective_genome_size@ | |
48 | |
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f5d67c722d67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
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49 --bw '${band_width}' |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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50 @mfold_command@ |
0 | 51 |
52 ## advanced options | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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53 #if $advanced_options.advanced_options_selector == "on": |
0 | 54 $advanced_options.nolambda |
55 $advanced_options.to_large | |
56 --ratio $advanced_options.ratio | |
57 --slocal $advanced_options.slocal | |
58 --llocal $advanced_options.llocal | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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59 #if $advanced_options.broad_options.broad_options_selector == "broad": |
0 | 60 --broad |
61 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }' | |
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e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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62 #else |
0 | 63 $advanced_options.broad_options.call_summits |
64 #end if | |
65 | |
66 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user": | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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67 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }' |
0 | 68 #else |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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69 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }' |
0 | 70 #end if |
71 | |
72 #end if | |
73 | |
74 ## With --bdg two additional output files will be generated. | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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75 #if "bdg" in str($outputs).split(','): |
0 | 76 --bdg |
77 #end if | |
78 | |
79 ## cutoff selection | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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80 #if str( $cutoff_options.cutoff_options_selector ) == "qvalue": |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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81 --qvalue '${ cutoff_options.qvalue }' |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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82 #elif str( $cutoff_options.cutoff_options_selector ) == "pvalue": |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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83 #if str($cutoff_options.pvalue).strip() != "": |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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84 --pvalue '${ cutoff_options.pvalue }' |
0 | 85 #end if |
86 #end if | |
87 | |
88 ## model options | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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89 #if $nomodel_type.nomodel_type_selector == "nomodel": |
0 | 90 --nomodel |
91 --extsize '${ nomodel_type.extsize }' | |
92 #end if | |
93 | |
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f5d67c722d67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
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94 2>&1 > $temp_stderr) |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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95 #if "peaks_tabular" in str($outputs).split(','): |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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96 && |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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97 cp MACS2_peaks.xls '${ output_tabular }' |
0 | 98 #end if |
99 | |
100 ## run R to create pdf from model script | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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101 #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(','): |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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102 && |
0 | 103 Rscript MACS2_model.r > MACS2_model.r.log |
104 #end if | |
105 | |
106 #if 'html' in str($outputs).split(','): | |
107 ## if output files exists, move them to the files_path and create a html result page linking to them | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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108 && |
0 | 109 ( |
110 count=`ls -1 MACS2* 2>/dev/null | wc -l`; | |
111 if [ \$count != 0 ]; | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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112 then |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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113 mkdir '${ output_extra_files.files_path }' && |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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114 cp MACS2* '${ output_extra_files.files_path }' && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
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115 python '$__tool_directory__/dir2html.py' |
f5d67c722d67
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
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116 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }'; |
0 | 117 fi; |
118 ) | |
119 #end if | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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120 && |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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121 exit_code_for_galaxy=\$? && |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
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122 cat $temp_stderr 2>&1 && |
0 | 123 (exit \$exit_code_for_galaxy) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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124 ]]></command> |
0 | 125 <inputs> |
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e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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126 <conditional name="treatment"> |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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127 <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" > |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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128 <option value="No" selected="True">No</option> |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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129 <option value="Yes">Yes</option> |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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130 </param> |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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131 <when value="No" > |
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132 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" /> |
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133 </when> |
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134 <when value="Yes"> |
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135 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" /> |
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136 </when> |
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137 </conditional> |
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138 |
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139 <conditional name="control"> |
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140 <param name="c_select" type="select" label="Do you have a Control File?" > |
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141 <option value="Yes" selected="True">Yes</option> |
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142 <option value="No">No</option> |
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143 </param> |
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144 <when value="Yes"> |
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145 <conditional name="c_multiple"> |
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146 <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" > |
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147 <option value="No" selected="True">No</option> |
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148 <option value="Yes">Yes</option> |
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149 </param> |
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150 <when value="No" > |
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151 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" /> |
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152 </when> |
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153 <when value="Yes"> |
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154 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Control File" /> |
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155 </when> |
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156 </conditional> |
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157 </when> |
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158 <when value="No" /> |
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159 </conditional> |
0 | 160 |
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161 <param name="bampe" type="boolean" truevalue="--format BAMPE" falsevalue="" checked="False" |
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162 label="Are your inputs Paired-end BAM files?" |
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163 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)"/> |
0 | 164 |
165 <expand macro="conditional_effective_genome_size" /> | |
166 <expand macro="band_width" /> | |
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167 <expand macro="mfold_options" /> |
0 | 168 |
169 <conditional name="cutoff_options"> | |
170 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value"> | |
171 <option value="qvalue" selected="true">q-value</option> | |
172 <option value="pvalue">p-value</option> | |
173 </param> | |
174 <when value="pvalue"> | |
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175 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection" help="default: not set (--pvalue)"/> |
0 | 176 </when> |
177 <when value="qvalue"> | |
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178 <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)"/> |
0 | 179 </when> |
180 </conditional> | |
181 | |
182 <conditional name="nomodel_type"> | |
183 <param name="nomodel_type_selector" type="select" label="Build Model"> | |
184 <option value="nomodel">Do not build the shifting model (--nomodel)</option> | |
185 <option value="create_model" selected="true">Build the shifting model</option> | |
186 </param> | |
187 <when value="create_model"/> | |
188 <when value="nomodel"> | |
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189 <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)."/> |
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190 <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 paired-end data (BAMPE). Default = 0 (--shift)."/> |
0 | 191 </when> |
192 </conditional> | |
193 | |
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194 <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built"> |
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195 <option value="peaks_tabular">Peaks as tabular file</option> |
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196 <option value="summits">Peak summits</option> |
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197 <option value="bdg" >Scores in bedGraph files (--bdg)</option> |
0 | 198 <option value="html">Summary page (html)</option> |
199 <option value="pdf">Plot in PDF</option> | |
200 </param> | |
201 | |
202 <conditional name="advanced_options"> | |
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203 <param name="advanced_options_selector" type="select" label="Advanced Options"> |
0 | 204 <option value="off" selected="true">Hide advanced options</option> |
205 <option value="on">Display advanced options</option> | |
206 </param> | |
207 <when value="on"> | |
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208 <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" |
0 | 209 label="When set, scale the small sample up to the bigger sample" |
210 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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211 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" |
0 | 212 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda)"/> |
213 <param name="ratio" type="float" value="1.0" | |
214 label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling" | |
215 help="(--ratio)"/> | |
216 <param name="slocal" value="1000" type="integer" label="The small nearby region in basepairs to calculate dynamic lambda" | |
217 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)"/> | |
218 <param name="llocal" value="10000" type="integer" label="The large nearby region in basepairs to calculate dynamic lambda" | |
219 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)"/> | |
220 <conditional name="broad_options"> | |
221 <param name="broad_options_selector" type="select" | |
222 label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)"> | |
223 <option value="nobroad" selected="true">No broad regions</option> | |
224 <option value="broad">broad regions</option> | |
225 </param> | |
226 <when value="broad"> | |
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227 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" |
0 | 228 help="value is either p-value or q-value as specified above (--broad-cutoff)"/> |
229 </when> | |
230 <when value="nobroad"> | |
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231 <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" |
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232 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region" |
0 | 233 help="(--call-summits)"/> |
234 </when> | |
235 </conditional> | |
236 <expand macro="keep_duplicates" /> | |
237 </when> | |
238 <when value="off" /> | |
239 </conditional> | |
240 </inputs> | |
241 <outputs> | |
242 <!--callpeaks output--> | |
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243 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)"> |
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244 <filter> outputs and 'peaks_tabular' in outputs</filter> |
0 | 245 </data> |
246 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)"> | |
247 <filter> | |
248 (( | |
249 advanced_options['advanced_options_selector'] == "on" and | |
250 advanced_options['broad_options']['broad_options_selector'] == "broad" | |
251 )) | |
252 </filter> | |
253 </data> | |
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254 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> |
0 | 255 <filter> |
256 (( | |
257 advanced_options['advanced_options_selector'] == "on" and | |
258 advanced_options['broad_options']['broad_options_selector'] == "broad" | |
259 )) | |
260 </filter> | |
261 </data> | |
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262 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)"> |
0 | 263 <filter> |
264 ( | |
265 advanced_options['advanced_options_selector'] == "off" or | |
266 ( | |
267 advanced_options['advanced_options_selector'] == "on" and | |
268 advanced_options['broad_options']['broad_options_selector'] == "nobroad" | |
269 )) | |
270 </filter> | |
271 </data> | |
272 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)"> | |
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273 <filter>outputs and 'summits' in outputs</filter> |
0 | 274 </data> |
275 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)"> | |
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276 <filter> |
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277 (( |
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278 outputs and 'pdf' in outputs and |
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279 nomodel_type['nomodel_type_selector'] == "create_model" |
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280 )) |
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281 </filter> |
0 | 282 </data> |
283 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)"> | |
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284 <filter>outputs and 'bdg' in outputs</filter> |
0 | 285 </data> |
286 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)"> | |
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287 <filter>outputs and 'bdg' in outputs</filter> |
0 | 288 </data> |
289 <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)"> | |
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290 <filter>outputs and 'html' in outputs</filter> |
0 | 291 </data> |
292 </outputs> | |
293 <tests> | |
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294 <test expect_num_outputs="5"> |
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295 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> |
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296 <param name="c_select" value="Yes"/> |
0 | 297 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> |
298 <param name="cutoff_options_selector" value="qvalue"/> | |
299 <param name="qvalue" value="0.05"/> | |
300 <param name="band_width" value="300"/> | |
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301 <param name="outputs" value="peaks_tabular,bdg,html"/> |
0 | 302 <param name="effective_genome_size_options_selector" value="user_defined" /> |
303 <param name="gsize" value="3300000000" /> | |
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304 <param name="lower" value="5" /> |
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305 <param name="upper" value="50" /> |
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306 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/> |
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307 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/> |
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308 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/> |
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309 <output name="output_extra_files"> |
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310 <assert_contents> |
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311 <has_text text="Additional output created by MACS2" /> |
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312 </assert_contents> |
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313 </output> |
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314 |
0 | 315 </test> |
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316 <!-- Ensure pdf can be output --> |
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317 <test expect_num_outputs="2"> |
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318 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> |
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319 <param name="c_select" value="Yes"/> |
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320 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> |
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321 <param name="cutoff_options_selector" value="qvalue"/> |
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322 <param name="qvalue" value="0.05"/> |
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323 <param name="band_width" value="300"/> |
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324 <param name="outputs" value="pdf"/> |
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325 <param name="effective_genome_size_options_selector" value="user_defined" /> |
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326 <param name="gsize" value="3300000000" /> |
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327 <param name="lower" value="5" /> |
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328 <param name="upper" value="50" /> |
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329 <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" /> |
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330 </test> |
0 | 331 </tests> |
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332 <help><![CDATA[ |
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333 |
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334 .. class:: infomark |
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335 |
0 | 336 **What it does** |
337 | |
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338 **callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. |
0 | 339 |
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340 .. _MACS2: https://github.com/taoliu/MACS |
0 | 341 |
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342 ----- |
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343 |
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344 **Inputs** |
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345 |
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346 MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended). |
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347 |
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348 A Treatment File is the only REQUIRED parameter for MACS. The file can be in BAM or BED format and this tool will autodetect the format using the first treatment file provided as input. If you have more than one alignment file per sample, you can select to pool them above. MACS can pool files together e.g. as `-t A B C` for treatment or `-c A B C` for control. |
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349 |
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350 Both single-end and paired-end mapping results can be input and you can specify if the data is from paired-end reads above. Paired-end mapping results can be input to MACS as a single BAM file, and just the left mate (5' end) tag will be automatically kept. However, when paired-end format (BAMPE) is specified, MACS will use the real fragments inferred from alignment results for reads pileup. |
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351 |
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352 ----- |
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353 |
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354 **Outputs** |
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355 |
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356 This tool produces a BED file of narrowPeaks as default output. It can also produce additional outputs, which can be selected under the **Additional Outputs** option above. |
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357 |
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358 * **a BED file of peaks** (default) |
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359 * a tabular file of peaks |
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360 * a BED file of peak summits |
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361 * two bedGraph files of scores, for treatment pileup and control lambda |
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362 * a HTML summary page |
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363 * a PDF plot (if model is built) |
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364 * a BED file of broad peaks (if **Composite broad regions** is selected under Advanced Options) |
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365 * a BED file of gapped peaks (if **Composite broad regions** is selected under Advanced Options) |
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366 |
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367 **Peaks BED File** |
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368 |
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369 The default output is the narrowPeak BED file (BED6+4 format). This contains the peak locations, together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser. |
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370 |
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371 Example: |
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372 |
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373 ======= ========= ======= ============ ==== === ======= ======== ======= ======= |
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374 1 2 3 4 5 6 7 8 9 **10** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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375 ======= ========= ======= ============ ==== === ======= ======== ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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376 chr1 840081 840400 MACS2_peak_1 69 . 4.89872 10.50944 6.91052 158 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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377 chr1 919419 919785 MACS2_peak_2 87 . 5.85158 12.44148 8.70936 130 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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378 chr1 937220 937483 MACS2_peak_3 66 . 4.87632 10.06728 6.61759 154 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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379 ======= ========= ======= ============ ==== === ======= ======== ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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380 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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381 Columns contain the following data: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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382 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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383 * **1st**: chromosome name |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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384 * **2nd**: start position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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385 * **3rd**: end position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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386 * **4th**: name of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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387 * **5th**: integer score for display in genome browser (e.g. UCSC) |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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388 * **6th**: strand, either "." (=no strand) or "+" or "-" |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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389 * **7th**: fold-change |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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390 * **8th**: -log10pvalue |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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391 * **9th**: -log10qvalue |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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392 * **10th**: relative summit position to peak start |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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393 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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394 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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395 **Peaks tabular File** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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396 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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397 A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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398 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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399 Example: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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400 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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401 ======= ========= ======= ========== ============== ========== ================== =================== ================== ============= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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402 **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)** **fold_enrichment** **-log10(qvalue)** **name** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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403 ======= ========= ======= ========== ============== ========== ================== =================== ================== ============= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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404 chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 MACS2_peak_1 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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405 chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 MACS2_peak_2 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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406 chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 MACS2_peak_3 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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407 ======= ========= ======= ========== ============== ========== ================== =================== ================== ============= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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408 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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409 Columns contain the following data: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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410 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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411 * **chr**: chromosome name |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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412 * **start**: start position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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413 * **end**: end position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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414 * **length**: length of peak region |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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415 * **abs_summit**: absolute peak summit position |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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416 * **pileup**: pileup height at peak summit |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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417 * **-log10(pvalue)**: -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10) |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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418 * **fold_enrichment**: fold enrichment for this peak summit against random Poisson distribution with local lambda |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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419 * **-log10(qvalue)**: -log10(qvalue) at peak summit |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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420 * **name**: name of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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421 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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422 *Note that these tabular file coordinates are 1-based which is different than the 0-based BED format (compare the start values in the BED and tabular Example above)* |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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423 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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424 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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425 **Summits BED File** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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426 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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427 A BED file which contains the peak summits locations for every peaks. The 5th column in this file is -log10qvalue, the same as in the Peaks BED file. If you want to find the motifs at the binding sites, this file is recommended. The file can be loaded directly to UCSC genome browser. Remove the beginning track line if you want to analyze it by other tools. |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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428 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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429 Example: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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430 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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431 ======= ========= ======= ============ ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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432 1 2 3 4 **5** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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433 ======= ========= ======= ============ ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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434 chr1 840239 840240 MACS2_peak_1 6.91052 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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435 chr1 919549 919550 MACS2_peak_2 8.70936 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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436 chr1 937374 937375 MACS2_peak_3 6.61759 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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437 ======= ========= ======= ============ ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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438 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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439 Columns contain the following data: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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440 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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441 * **1st**: chromosome name |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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442 * **2nd**: start position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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443 * **3rd**: end position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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444 * **4th**: name of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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445 * **5th**: -log10qvalue |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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446 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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447 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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448 **BedGraph Files** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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449 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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450 MACS2 will output two kinds of bedGraph files if the --bdg option is selected under the Additional Outputs option above, which contain the scores for the treatment fragment pileup and control local lambda, respectively. BedGraph files can be imported into genome browsers, such as UCSC genome browser, or be converted into even smaller bigWig files. For more information on bedGraphs, see the `UCSC website here`_. |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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451 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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7
diff
changeset
|
452 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
453 Example: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
454 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
455 **Treatment pileup file** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
456 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
457 ======= ========= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
458 1 2 3 **4** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
459 ======= ========= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
460 chr1 840146 840147 3.00000 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
461 chr1 840147 840332 4.00000 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
462 chr1 840332 840335 3.00000 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
463 ======= ========= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
464 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
465 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
466 **Control lambda file** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
467 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
468 ======= ========= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
469 1 2 3 **4** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
470 ======= ========= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
471 chr1 800953 801258 0.02536 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
472 chr1 801258 801631 0.25364 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
473 chr1 801631 801885 0.99858 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
474 ======= ========= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
475 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
476 Columns contain the following data: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
477 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
478 * **1st**: chromosome name |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
479 * **2nd**: start position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
480 * **3rd**: end position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
481 * **4th**: treatment pileup score or control local lambda score |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
482 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
483 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
484 **Broad peaks File** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
485 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
486 If the broad option (--broad) is selected unded Advanced Options above, MACS2 will output a broadPeaks file. When this flag is on, MACS will try to composite broad regions in BED12 ( a gene-model-like format ) by putting nearby highly enriched regions into a broad region with loose cutoff. The broad region is controlled by another cutoff through --broad-cutoff. The maximum length of broad region length is 4 times of d from MACS. The broad peaks file is in BED6+3 format which is similar to the narrowPeak file, except for missing the 10th column for annotating peak summits. |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
487 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
488 Example: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
489 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
490 ======= ========= ======= ============ ==== === ======= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
491 1 2 3 4 5 6 7 8 9 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
492 ======= ========= ======= ============ ==== === ======= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
493 chr1 840081 840400 MACS2_peak_1 52 . 4.08790 8.57605 5.21506 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
494 chr1 919419 919785 MACS2_peak_2 56 . 4.37270 8.90436 5.60462 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
495 chr1 937220 937483 MACS2_peak_3 48 . 4.02343 8.06676 4.86861 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
496 ======= ========= ======= ============ ==== === ======= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
497 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
498 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
499 Columns contain the following data: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
500 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
501 * **1st**: chromosome name |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
502 * **2nd**: start position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
503 * **3rd**: end position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
504 * **4th**: name of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
505 * **5th**: integer score for display in genome browser (e.g. UCSC) |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
506 * **6th**: strand, either "." (=no strand) or "+" or "-" |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
507 * **7th**: fold-change |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
508 * **8th**: -log10pvalue |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
509 * **9th**: -log10qvalue |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
510 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
511 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
512 **Gapped peaks File** |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
513 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
514 If the broad option (--broad) is selected unded Advanced Options above, MACS2 will also output a gappedPeaks file. The gappedPeak file is in BED12+3 format and contains both the broad region and narrow peaks. The file can be loaded directly to UCSC genome browser. |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
515 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
516 Example: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
517 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
518 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
519 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
520 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
521 chr1 840081 840400 MACS2_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
522 chr1 919419 919785 MACS2_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
523 chr1 937220 937483 MACS2_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
524 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= ======= |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
525 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
526 Columns contain the following data: |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
527 |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
528 * **1st**: chromosome name |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
529 * **2nd**: start position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
|
530 * **3rd**: end position of peak |
e8a060164e11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents:
7
diff
changeset
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531 * **4th**: name of peak |
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532 * **5th**: 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser |
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533 * **6th**: strand, either "." (=no strand) or "+" or "-" |
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534 * **7th**: start of the first narrow peak in the region |
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535 * **8th**: end of the peak |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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536 * **9th**: RGB color key, default colour is 0 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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537 * **10th**: number of blocks, including the starting 1bp and ending 1bp of broad regions |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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538 * **11th**: length of each block, comma-separated values if multiple |
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539 * **12th**: start of each block, comma-separated values if multiple |
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540 * **13th**: fold-change |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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541 * **14th**: -log10pvalue |
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542 * **15th**: -log10qvalue |
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543 |
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544 ----- |
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545 |
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546 **More Information** |
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547 |
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548 MACS2 performs the following analysis steps: |
0 | 549 |
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550 * Artificially extends reads to expected fragment length, and generates coverage map along genome. |
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551 * Assumes 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. |
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552 * For a given location, asks do we see more reads than we would have expected from the Poisson (p < 0.00005)? If Yes, MACS2 calls a peak. |
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553 |
0 | 554 |
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555 **Tips of fine-tuning peak calling** |
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556 |
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557 Check out these other MACS2 tools: |
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558 |
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559 * **MACS2 bdgcmp** can be used on the callpeak bedGraph files or bedGraph files from other resources to calculate score track. |
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560 * **MACS2 bdgpeakcall** can be used on the file generated from bdgcmp or bedGraph file from other resources to call peaks with given cutoff, maximum-gap between nearby mergable peaks and minimum length of peak. bdgbroadcall works similarly to bdgpeakcall, however it will output a broad peaks file in BED12 format. |
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561 * Differential calling tool **MACS2 bdgdiff**, can be used on 4 bedGraph files which are scores between treatment 1 and control 1, treatment 2 and control 2, treatment 1 and treatment 2, treatment 2 and treatment 1. It will output the consistent and unique sites according to parameter settings for minimum length, maximum gap and cutoff. |
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562 |
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563 .. class:: warningmark |
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564 |
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565 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. For more information, see the MACS2_ website. |
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567 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html |
0 | 568 |
569 @citation@ | |
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570 ]]></help> |
0 | 571 <expand macro="citations" /> |
572 </tool> |