Mercurial > repos > iuc > macs2

annotate macs2_callpeak.xml @ 52:6c9ea5f92ddb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
author iuc
date Wed, 27 Dec 2017 10:17:42 -0500
parents 61d2f23acfb8
children 8f6b37d29df5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.1">
33
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" />
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
10 <command><![CDATA[
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
11 #set $temp_stderr = 'macs2_stderr'
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
12 (macs2 callpeak
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
13
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
14 --name 'MACS2'
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
15
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
16 ## Treatment File(s)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
17
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
18 #if str($treatment.t_multi_select) == "Yes":
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
19 -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), '$treatment.input_treatment_file' ) ) }
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
20
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
21 #if '$treatment.input_treatment_file[0].ext.upper()' == "BAM" and $bampe:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
22 --format BAMPE
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
23 #else
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
24 --format='$treatment.input_treatment_file[0].ext.upper()'
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
25 #end if
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
26
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
27 #else
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
28 -t '$treatment.input_treatment_file'
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
29
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
30 #if '$treatment.input_treatment_file.ext.upper()' == "BAM" and $bampe:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
31 --format BAMPE
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
32 #else
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
33 --format='$treatment.input_treatment_file.ext.upper()'
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
34 #end if
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
35 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
36
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
37 ## Control File(s)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
38
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
39 #if str($control.c_select) == "Yes":
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
40 #if str($control.c_multiple.c_multi_select) == "Yes":
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
41 -c ${ ' '.join( map( lambda x:'"%s"' % ( x ), '$control.c_multiple.input_control_file' ) ) }
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
42 #else
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
43 -c '$control.c_multiple.input_control_file'
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
44 #end if
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
45 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
46
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
47 @effective_genome_size@
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
48
51
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 50
diff changeset
49 --bw '${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
50 @mfold_command@
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
51
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
52 ## 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
53 #if $advanced_options.advanced_options_selector == "on":
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
54 $advanced_options.nolambda
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
55 $advanced_options.to_large
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
56 --ratio $advanced_options.ratio
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
57 --slocal $advanced_options.slocal
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
58 --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
59 #if $advanced_options.broad_options.broad_options_selector == "broad":
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
60 --broad
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
61 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
62 #else
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
63 $advanced_options.broad_options.call_summits
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
64 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
65
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
66 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
67 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
68 #else
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
69 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
70 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
71
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
72 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
73
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
74 ## With --bdg two additional output files will be generated.
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
75 #if "bdg" in str($outputs).split(','):
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
76 --bdg
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
77 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
78
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
79 ## 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
80 #if str( $cutoff_options.cutoff_options_selector ) == "qvalue":
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
81 --qvalue '${ 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
82 #elif str( $cutoff_options.cutoff_options_selector ) == "pvalue":
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
83 #if str($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
84 --pvalue '${ cutoff_options.pvalue }'
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
85 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
86 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
87
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
88 ## 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
89 #if $nomodel_type.nomodel_type_selector == "nomodel":
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
90 --nomodel
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
91 --extsize '${ nomodel_type.extsize }'
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
92 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
93
51
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 50
diff changeset
94 2>&1 > $temp_stderr)
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
95 #if "peaks_tabular" in str($outputs).split(','):
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
96 &&
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_peaks.xls '${ output_tabular }'
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
98 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
99
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
100 ## 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
101 #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
102 &&
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
103 Rscript MACS2_model.r > MACS2_model.r.log
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
104 #end if
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
105
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
106 #if 'html' in str($outputs).split(','):
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
107 ## if output files exists, move them to the files_path and create a html result page linking to them
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
108 &&
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
109 (
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
110 count=`ls -1 MACS2* 2>/dev/null | wc -l`;
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
111 if [ \$count != 0 ];
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
112 then
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
113 mkdir '${ 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
114 cp MACS2* '${ output_extra_files.files_path }' &&
51
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 50
diff changeset
115 python '$__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
116 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }';
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
117 fi;
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
118 )
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
119 #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
120 &&
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
121 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
122 cat $temp_stderr 2>&1 &&
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
123 (exit \$exit_code_for_galaxy)
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
124 ]]></command>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
125 <inputs>
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
126 <conditional name="treatment">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
127 <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
128 <option value="No" selected="True">No</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
129 <option value="Yes">Yes</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
130 </param>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
131 <when value="No" >
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
132 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" />
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
133 </when>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
134 <when value="Yes">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
135 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" />
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
136 </when>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
137 </conditional>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
138
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
139 <conditional name="control">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
140 <param name="c_select" type="select" label="Do you have a Control File?" >
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
141 <option value="Yes" selected="True">Yes</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
142 <option value="No">No</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
143 </param>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
144 <when value="Yes">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
145 <conditional name="c_multiple">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
146 <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" >
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
147 <option value="No" selected="True">No</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
148 <option value="Yes">Yes</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
149 </param>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
150 <when value="No" >
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
151 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" />
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
152 </when>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
153 <when value="Yes">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
154 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Control File" />
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
155 </when>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
156 </conditional>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
157 </when>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
158 <when value="No" />
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
159 </conditional>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
160
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
161 <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
162 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
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)"/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
164
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
165 <expand macro="conditional_effective_genome_size" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
166 <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
167 <expand macro="mfold_options" />
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
168
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
169 <conditional name="cutoff_options">
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
170 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
171 <option value="qvalue" selected="true">q-value</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
172 <option value="pvalue">p-value</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
173 </param>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
174 <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
175 <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
176 </when>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
177 <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
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)"/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
179 </when>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
180 </conditional>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
181
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
182 <conditional name="nomodel_type">
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
183 <param name="nomodel_type_selector" type="select" label="Build Model">
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
184 <option value="nomodel">Do not build the shifting model (--nomodel)</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
185 <option value="create_model" selected="true">Build the shifting model</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
186 </param>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
187 <when value="create_model"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
188 <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
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)."/>
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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)."/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
191 </when>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
192 </conditional>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
193
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
195 <option value="peaks_tabular">Peaks as tabular file</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
196 <option value="summits">Peak summits</option>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
197 <option value="bdg" >Scores in bedGraph files (--bdg)</option>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
198 <option value="html">Summary page (html)</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
199 <option value="pdf">Plot in PDF</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
200 </param>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
201
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
202 <conditional name="advanced_options">
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
203 <param name="advanced_options_selector" type="select" label="Advanced Options">
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
204 <option value="off" selected="true">Hide advanced options</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
205 <option value="on">Display advanced options</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
206 </param>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
207 <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
208 <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False"
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
209 label="When set, scale the small sample up to the bigger sample"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
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)"/>
36
8c8ae1e19b10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents: 33
diff changeset
211 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False"
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
212 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
213 <param name="ratio" type="float" value="1.0"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
214 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
215 help="(--ratio)"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
216 <param name="slocal" value="1000" type="integer" label="The small nearby region in basepairs to calculate dynamic lambda"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
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)"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
218 <param name="llocal" value="10000" type="integer" label="The large nearby region in basepairs to calculate dynamic lambda"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
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)"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
220 <conditional name="broad_options">
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
221 <param name="broad_options_selector" type="select"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
222 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
223 <option value="nobroad" selected="true">No broad regions</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
224 <option value="broad">broad regions</option>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
225 </param>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
226 <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
227 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
228 help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
229 </when>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
230 <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
231 <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
232 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
233 help="(--call-summits)"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
234 </when>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
235 </conditional>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
236 <expand macro="keep_duplicates" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
237 </when>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
238 <when value="off" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
239 </conditional>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
240 </inputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
241 <outputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
242 <!--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
243 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)">
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
244 <filter> outputs and 'peaks_tabular' in outputs</filter>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
245 </data>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
246 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
247 <filter>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
248 ((
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
249 advanced_options['advanced_options_selector'] == "on" and
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
250 advanced_options['broad_options']['broad_options_selector'] == "broad"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
251 ))
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
252 </filter>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
253 </data>
47
9033b59bf9c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 44
diff changeset
254 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
255 <filter>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
256 ((
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
257 advanced_options['advanced_options_selector'] == "on" and
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
258 advanced_options['broad_options']['broad_options_selector'] == "broad"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
259 ))
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
260 </filter>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
261 </data>
47
9033b59bf9c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 44
diff changeset
262 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
263 <filter>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
264 (
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
265 advanced_options['advanced_options_selector'] == "off" or
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
266 (
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
267 advanced_options['advanced_options_selector'] == "on" and
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
268 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
269 ))
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
270 </filter>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
271 </data>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
272 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
273 <filter>outputs and 'summits' in outputs</filter>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
274 </data>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
275 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
44
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 36
diff changeset
276 <filter>
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 36
diff changeset
277 ((
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
278 outputs and 'pdf' in outputs and
44
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 36
diff changeset
279 nomodel_type['nomodel_type_selector'] == "create_model"
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 36
diff changeset
280 ))
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 36
diff changeset
281 </filter>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
282 </data>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
283 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
284 <filter>outputs and 'bdg' in outputs</filter>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
285 </data>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
286 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)">
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
287 <filter>outputs and 'bdg' in outputs</filter>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
288 </data>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
289 <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)">
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
290 <filter>outputs and 'html' in outputs</filter>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
291 </data>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
292 </outputs>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
293 <tests>
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
294 <test expect_num_outputs="5">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
295 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
296 <param name="c_select" value="Yes"/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
297 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
298 <param name="cutoff_options_selector" value="qvalue"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
299 <param name="qvalue" value="0.05"/>
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
300 <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
301 <param name="outputs" value="peaks_tabular,bdg,html"/>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
302 <param name="effective_genome_size_options_selector" value="user_defined" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
303 <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
304 <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
305 <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
306 <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
307 <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
308 <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
309 <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
310 <assert_contents>
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 50
diff changeset
311 <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
312 </assert_contents>
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 50
diff changeset
313 </output>
61d2f23acfb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
iuc
parents: 50
diff changeset
314
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
315 </test>
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
316 <!-- Ensure pdf can be output -->
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
317 <test expect_num_outputs="2">
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
318 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
319 <param name="c_select" value="Yes"/>
44
37f53bf6c2b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents: 36
diff changeset
320 <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
321 <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
322 <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
323 <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
324 <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
325 <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
326 <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
327 <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
328 <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
329 <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
330 </test>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
331 </tests>
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
332 <help><![CDATA[
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
333
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
334 .. class:: infomark
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
335
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
336 **What it does**
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
337
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
339
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
340 .. _MACS2: https://github.com/taoliu/MACS
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
341
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
342 -----
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
343
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
344 **Inputs**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
345
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
346 MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended).
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
347
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
349
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
351
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
352 -----
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
353
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
354 **Outputs**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
355
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
357
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
358 * **a BED file of peaks** (default)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
359 * a tabular file of peaks
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
360 * a BED file of peak summits
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
361 * two bedGraph files of scores, for treatment pileup and control lambda
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
362 * a HTML summary page
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
363 * a PDF plot (if model is built)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
364 * a BED file of broad peaks (if **Composite broad regions** is selected under Advanced Options)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
365 * a BED file of gapped peaks (if **Composite broad regions** is selected under Advanced Options)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
366
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
367 **Peaks BED File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
368
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
370
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
371 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
372
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
373 ======= ========= ======= ============ ==== === ======= ======== ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
374 1 2 3 4 5 6 7 8 9 **10**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
375 ======= ========= ======= ============ ==== === ======= ======== ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
376 chr1 840081 840400 MACS2_peak_1 69 . 4.89872 10.50944 6.91052 158
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
377 chr1 919419 919785 MACS2_peak_2 87 . 5.85158 12.44148 8.70936 130
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
378 chr1 937220 937483 MACS2_peak_3 66 . 4.87632 10.06728 6.61759 154
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
379 ======= ========= ======= ============ ==== === ======= ======== ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
380
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
381 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
382
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
383 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
384 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
385 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
386 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
387 * **5th**: integer score for display in genome browser (e.g. UCSC)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
388 * **6th**: strand, either "." (=no strand) or "+" or "-"
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
389 * **7th**: fold-change
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
390 * **8th**: -log10pvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
391 * **9th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
392 * **10th**: relative summit position to peak start
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
393
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
394
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
395 **Peaks tabular File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
396
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
397 A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
398
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
399 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
400
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
401 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
402 **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)** **fold_enrichment** **-log10(qvalue)** **name**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
403 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
404 chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 MACS2_peak_1
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
405 chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 MACS2_peak_2
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
406 chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 MACS2_peak_3
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
407 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
408
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
409 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
410
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
411 * **chr**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
412 * **start**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
413 * **end**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
414 * **length**: length of peak region
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
415 * **abs_summit**: absolute peak summit position
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
416 * **pileup**: pileup height at peak summit
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
417 * **-log10(pvalue)**: -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
418 * **fold_enrichment**: fold enrichment for this peak summit against random Poisson distribution with local lambda
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
419 * **-log10(qvalue)**: -log10(qvalue) at peak summit
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
420 * **name**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
421
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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)*
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
423
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
424
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
425 **Summits BED File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
426
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
428
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
429 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
430
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
431 ======= ========= ======= ============ =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
432 1 2 3 4 **5**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
433 ======= ========= ======= ============ =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
434 chr1 840239 840240 MACS2_peak_1 6.91052
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
435 chr1 919549 919550 MACS2_peak_2 8.70936
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
436 chr1 937374 937375 MACS2_peak_3 6.61759
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
437 ======= ========= ======= ============ =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
438
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
439 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
440
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
441 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
442 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
443 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
444 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
445 * **5th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
446
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
447
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
448 **BedGraph Files**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
449
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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`_.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
451
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
452
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
453 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
454
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
455 **Treatment pileup file**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
456
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
457 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
458 1 2 3 **4**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
459 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
460 chr1 840146 840147 3.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
461 chr1 840147 840332 4.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
462 chr1 840332 840335 3.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
463 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
464
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
465
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
466 **Control lambda file**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
467
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
468 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
469 1 2 3 **4**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
470 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
471 chr1 800953 801258 0.02536
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
472 chr1 801258 801631 0.25364
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
473 chr1 801631 801885 0.99858
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
474 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
475
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
476 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
477
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
478 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
479 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
480 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
481 * **4th**: treatment pileup score or control local lambda score
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
482
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
483
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
484 **Broad peaks File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
485
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
487
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
488 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
489
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
490 ======= ========= ======= ============ ==== === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
491 1 2 3 4 5 6 7 8 9
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
492 ======= ========= ======= ============ ==== === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
493 chr1 840081 840400 MACS2_peak_1 52 . 4.08790 8.57605 5.21506
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
494 chr1 919419 919785 MACS2_peak_2 56 . 4.37270 8.90436 5.60462
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
495 chr1 937220 937483 MACS2_peak_3 48 . 4.02343 8.06676 4.86861
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
496 ======= ========= ======= ============ ==== === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
497
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
498
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
499 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
500
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
501 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
502 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
503 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
504 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
505 * **5th**: integer score for display in genome browser (e.g. UCSC)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
506 * **6th**: strand, either "." (=no strand) or "+" or "-"
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
507 * **7th**: fold-change
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
508 * **8th**: -log10pvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
509 * **9th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
510
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
511
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
512 **Gapped peaks File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
513
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
515
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
516 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
517
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
518 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
519 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
520 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
521 chr1 840081 840400 MACS2_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
522 chr1 919419 919785 MACS2_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
523 chr1 937220 937483 MACS2_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
524 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
525
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
526 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
527
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
528 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
529 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
530 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
531 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
532 * **5th**: 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
533 * **6th**: strand, either "." (=no strand) or "+" or "-"
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
534 * **7th**: start of the first narrow peak in the region
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
535 * **8th**: end of the peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
536 * **9th**: RGB color key, default colour is 0
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
537 * **10th**: number of blocks, including the starting 1bp and ending 1bp of broad regions
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
538 * **11th**: length of each block, comma-separated values if multiple
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
539 * **12th**: start of each block, comma-separated values if multiple
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
540 * **13th**: fold-change
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
541 * **14th**: -log10pvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
542 * **15th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
543
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
544 -----
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
545
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
546 **More Information**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
547
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
548 MACS2 performs the following analysis steps:
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
549
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
550 * Artificially extends reads to expected fragment length, and generates coverage map along genome.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
553
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
554
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
555 **Tips of fine-tuning peak calling**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
556
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
557 Check out these other MACS2 tools:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
558
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
559 * **MACS2 bdgcmp** can be used on the callpeak bedGraph files or bedGraph files from other resources to calculate score track.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
49
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
562
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
563 .. class:: warningmark
1b3f899ef044 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 48
diff changeset
564
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
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.
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
566
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
567 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
568
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
569 @citation@
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
570 ]]></help>
33
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
571 <expand macro="citations" />
c82a1f154c60 Uploaded
iuc
parents:
diff changeset
572 </tool>