Mercurial > repos > iuc > genrich

annotate genrich.xml @ 1:65ea5e60e6b0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
author iuc
date Sat, 17 Aug 2019 16:23:09 -0400
parents 48c5ff6b11fb
children bb2fb6a25c21
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
1 <tool id="genrich" name="Genrich" version="0.5+galaxy1">
0
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
2 <description>Detecting sites of genomic enrichment</description>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
3 <requirements>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
4 <requirement type="package" version="0.5">genrich</requirement>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
5 <requirement type="package" version="1.9">samtools</requirement>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
6 </requirements>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
7
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
8 <version_command>Genrich --version</version_command>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
9
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
11
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
12 #set $file_stderr = 'genrich_stderr'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
13
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
14 Genrich
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
15
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
16 ###########
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
17 ## Input ##
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
18 ###########
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
19
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
20 ## Treatment File(s)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
21 #if str($treatment.t_multi_select) == "Yes":
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
22 -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) }
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
23 #else
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
24 -t '$treatment.input_treatment_file'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
25 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
26
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
27 ## Control File(s)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
28 #if str($control.c_select) == "Yes":
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
29 #if str($control.c_multiple.c_multi_select) == "Yes":
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
30 -c ${ ' '.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) }
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
31 #else
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
32 -c '$control.c_multiple.input_control_file'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
33 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
34 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
35
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
36 ####################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
37 ## Filter Options ##
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
38 ####################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
39
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
40 #if $filter_options.duplicates:
1
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
41 -r -R '${out_dups}'
0
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
42 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
43
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
44 #if $filter_options.exclude_chr:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
45 -e '$filter_options.exclude_chr'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
46 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
47
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
48 #if str($cond_exclude.exclude_select) == "Yes":
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
49 -E $cond_exclude.erf
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
50 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
51
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
52 -m $filter_options.min_mapq
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
53 -s $filter_options.alignment_score
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
54 $filter_options.unpaired
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
55
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
56 #if $filter_options.alignment_lengths:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
57 -w $filter_options.alignment_lengths
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
58 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
59
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
60 $filter_options.alignment_lengths2
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
61
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
62 ##################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
63 ## ATAC Options ##
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
64 ##################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
65
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
66 $atac_options.atac
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
67 -d $atac_options.expand_sites
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
68
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
69 #########################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
70 ## Peakcalling Options ##
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
71 #########################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
72
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
73 -q $peakcalling_options.max_q
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
74
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
75 #if $peakcalling_options.max_p:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
76 -p $peakcalling_options.max_p
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
77 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
78
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
79 -a $peakcalling_options.min_auc
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
80 -l $peakcalling_options.min_peak_length
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
81 -g $peakcalling_options.max_dist
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
82
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
83 ###################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
84 ## Other Options ##
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
85 ###################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
86
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
87 $other_options.skip_peak_calling
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
88 -v
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
89
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
90 ####################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
91 ## Output Options ##
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
92 ####################
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
93
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
94 #if $output_options.bedgraph1:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
95 -f '${out_bedgraph1}'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
96 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
97
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
98 #if $output_options.bedgraph2:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
99 -k '${out_bedgraph2}'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
100 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
101
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
102 #if $output_options.bed:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
103 -b '${out_bed}'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
104 #end if
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
105
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
106 -o '${outfile}'
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
107
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
108 2>&1 > $file_stderr &&
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
109 exit_code_for_galaxy=\$? &&
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
110 cat $file_stderr 2>&1 &&
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
111 exit \$exit_code_for_galaxy
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
112
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
113 ]]></command>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
114 <inputs>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
115 <conditional name="treatment">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
116 <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
117 <option value="No" selected="True">No</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
118 <option value="Yes">Yes</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
119 </param>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
120 <when value="No" >
1
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
121 <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File"
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
122 help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
0
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
123 </when>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
124 <when value="Yes">
1
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
125 <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true"
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
126 label="Treatment Files."
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
127 help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
0
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
128 </when>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
129 </conditional>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
130
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
131 <conditional name="control">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
132 <param name="c_select" type="select" label="Do you have a Control File?" >
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
133 <option value="Yes">Yes</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
134 <option value="No" selected="True">No</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
135 </param>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
136 <when value="Yes">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
137 <conditional name="c_multiple">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
138 <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" >
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
139 <option value="No" selected="True">No</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
140 <option value="Yes">Yes</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
141 </param>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
142 <when value="No" >
1
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
143 <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File"
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
144 help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
0
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
145 </when>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
146 <when value="Yes">
1
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
147 <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files"
65ea5e60e6b0 "planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
iuc
parents: 0
diff changeset
148 help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
0
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
149 </when>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
150 </conditional>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
151 </when>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
152 <when value="No" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
153 </conditional>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
154
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
155 <!-- Filter Options -->
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
156 <conditional name="cond_exclude">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
157 <param name="exclude_select" type="select" label="Do you have a BED file of genomic regions to exclude?" help="Input BED file of genomic regions to exclude." >
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
158 <option value="No" selected="True">No</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
159 <option value="Yes">Yes</option>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
160 </param>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
161 <when value="No" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
162 <when value="Yes">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
163 <param name="erf" argument="-E" type="data" format="bed" label="BED File" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
164 </when>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
165 </conditional>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
166
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
167 <section name="filter_options" title="Filter Options">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
168 <param name="duplicates" argument="-r" type="boolean" value="False" truevalue="-r -R" falsevalue="" label="Remove PCR duplicates" help="In this process, it analyzes reads/fragments based on their alignments, in three separate groups (proper pairs, discordant pairs, and singletons), and removes those identified as duplicates from further analysis. One novel feature is that this evaluation takes into account reads/fragments with multiple alignments."/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
169 <param name="exclude_chr" argument="-e" type="text" optional="True" label="Comma-separated list of chromosomes to exclude" help="All alignments to the given list of chromosomes (reference sequences) are excluded from peak-calling. More details can be found in the tool description.">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
170 <sanitizer>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
171 <valid initial="string.printable">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
172 <remove value="&apos;"/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
173 </valid>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
174 </sanitizer>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
175 </param>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
176 <param name="min_mapq" argument="-m" type="integer" min="0" value="0" label="Minimum MAPQ to keep an alignment." help="All alignments with MAPQ less than the given value are eliminated. This is equivalent to filtering with samtools view -q. This option should not be used if the SAM/BAM lists multiple alignments for some reads/fragments. Instead, filtering should be accomplished via -s. (def. 0)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
177 <param name="alignment_score" argument="-s" type="float" min="0.0" value="0.0" label="Keep sec alns with AS >= bestAS." help="Genrich considers all secondary alignments of multimapping reads, but, by default, it keeps only the alignments whose scores are equal to the best score for the read/fragment. Setting a value such as -s 20 causes Genrich also to keep secondary alignments whose scores are within 20 of the best. (def. 0)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
178 <param name="unpaired" argument="-y" type="boolean" value="False" truevalue="-y" falsevalue="" label="Keep unpaired alignments." help="Unpaired alignments are kept, just as they appear in the SAM/BAM. (def. false)"/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
179 <param name="alignment_lengths" argument="-w" type="integer" min="1" optional="True" value="" label="Keep unpaired alignments with a certain length." help="Unpaired alignments are kept, with their lengths changed to the given value (from their 5' ends). (def. not defined)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
180 <param name="alignment_lengths2" argument="-x" type="boolean" value="False" truevalue="-x" falsevalue="" label="Keep unpaired alns, lengths changed to paired average." help="Unpaired alignments are kept, with their lengths changed to the average length of fragments inferred from properly paired alignments (excluding those aligning to skipped chromosomes [-e]). (def. not defined)"/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
181 </section>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
182
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
183 <!-- ATAC Options -->
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
184 <section name="atac_options" title="ATAC Options">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
185 <param name="atac" argument="-j" type="boolean" value="False" truevalue="-j" falsevalue="" label="Use ATAC-seq mode." help="Use ATAC-seq mode (def. false)"/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
186 <param name="expand_sites" argument="-d" type="integer" min="0" value="100" label="Expand cut sites." help="Expand cut sites to x bp (def. 100)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
187 </section>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
188
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
189 <!-- Peakcalling Options -->
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
190 <section name="peakcalling_options" title="Peakcalling Options">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
191 <param name="max_q" argument="-q" type="float" min="0.0" max="1.0" value="0.05" label="Maximum q-value." help="Maximum q-value (FDR-adjusted p-value). These parameters establish the statistical threshold below which a base is considered significantly enriched in the experimental sample(s) vs. the control/background. The significance value is automatically converted to a -log10 scale by Genrich. (def. 0.05)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
192 <param name="max_p" argument="-p" type="float" min="0" max="1.0" optional="True" value="" label="Maximum p-value." help="When -p is selected, q-values are not calculated (reported as -1). (def. turned off)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
193 <param name="min_auc" argument="-a" type="float" min="0" value="20.0" label="Minimum AUC for a peak." help="Minimum AUC for a peak. (def. 20.0)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
194 <param name="min_peak_length" argument="-l" type="integer" min="0" value="0" label="Minimum length of a peak." help="With this option, any potential peak whose length is below the specified value is discarded, regardless of its significance. The default of 0 means that no peaks are eliminated on this basis. (def. 0)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
195 <param name="max_dist" argument="-g" type="integer" min="0" value="100" label="Maximum distance between signif. sites." help="This parameter sets the maximum distance between sites that achieve significance in order for them to be linked together into the same potential peak. (def. 100)" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
196 </section>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
197
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
198 <!-- Other Options -->
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
199 <section name="other_options" title="Other Options">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
200 <param name="skip_peak_calling" argument="-X" type="boolean" value="False" truevalue="-X" falsevalue="" label="Skip peak-calling." help="This is a convenience option for those who are unsure of the peak-calling parameters but do not want to run the full analysis multiple times. Genrich interprets the alignment files (including identifying PCR duplicates) and produces intermediate log files, but does not perform the peak-calling step."/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
201 </section>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
202
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
203 <!-- Output Options -->
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
204 <section name="output_options" title="Output Options">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
205 <param name="bedgraph1" argument="-f" type="boolean" value="False" label="Bedgraph-ish p/q Values" help="Output bedgraph-ish file for p/q values."/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
206 <param name="bedgraph2" argument="-k" type="boolean" value="False" label="Bedgraph-ish Pileups" help="Output bedgraph-ish file for pileups and p-values."/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
207 <param name="bed" argument="-b" type="boolean" value="False" label="Bed File" help="Output BED file for reads/fragments/intervals."/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
208 </section>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
209 </inputs>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
210
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
211
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
212 <outputs>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
213 <data name="outfile" format="encodepeak" label="${tool.name} on ${on_string}"/>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
214
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
215 <data name="out_bedgraph1" format="bedgraph" from_work_dir="*.bedgraph" label="${tool.name} on ${on_string}: Bedgraph p/q">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
216 <filter>(output_options['bedgraph1'] is True)</filter>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
217 </data>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
218 <data name="out_bedgraph2" format="bedgraph" from_work_dir="*.bedgraph" label="${tool.name} on ${on_string}: Bedgraph Pileups">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
219 <filter>(output_options['bedgraph2'] is True)</filter>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
220 </data>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
221 <data name="out_bed" format="bed" from_work_dir="*.bed" label="${tool.name} on ${on_string}: Bed reads/fragments/intervals">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
222 <filter>(output_options['bed'] is True)</filter>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
223 </data>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
224 <data name="out_dups" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: PCR duplicates">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
225 <filter>(filter_options['duplicates'] is True)</filter>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
226 </data>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
227 </outputs>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
228 <tests>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
229 <!-- ATAC Test Data -->
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
230 <test expect_num_outputs="4">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
231 <param name="input_treatment_file" ftype="bam" value="atac_test.bam" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
232 <param name="atac" value="True" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
233 <param name="bedgraph1" value="True" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
234 <param name="bedgraph2" value="True" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
235 <param name="bed" value="True" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
236 <output name="outfile" ftype="encodepeak" file="atac_out.encodepeak" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
237 <output name="out_bedgraph1" ftype="bedgraph" file="atac_out2.bedgraph" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
238 <output name="out_bedgraph2" ftype="bedgraph" file="atac_out3.bedgraph" compare="contains" lines_diff="1" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
239 <output name="out_bed" ftype="bed" file="atac_out4.bed" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
240 </test>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
241 <!-- ChIP Test Data with Control-->
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
242 <test expect_num_outputs="4">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
243 <param name="input_treatment_file" ftype="bam" value="CTCF_PE_ChIP_chr22.bam" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
244 <param name="input_control_file" ftype="bam" value="CTCF_PE_CTRL_chr22.bam" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
245 <param name="c_select" value="Yes" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
246 <param name="bedgraph1" value="True" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
247 <param name="bedgraph2" value="True" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
248 <param name="bed" value="True" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
249 <output name="outfile" ftype="encodepeak" file="CTCF.encodepeak" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
250 <output name="out_bedgraph1" ftype="bedgraph" file="CTCF1.bedgraph" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
251 <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
252 <output name="out_bed" ftype="bed" file="CTCF.bed" />
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
253 </test>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
254 </tests>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
255 <help><![CDATA[
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
256
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
257 .. class:: infomark
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
258
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
259 **What it does**
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
260
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
261 -------------------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
262
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
263 **Genrich** Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
264
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
265 ATAC-seq is a method for assessing genomic regions of open chromatin. Since only the ends of the DNA fragments indicate where the transposase enzyme was able to insert into the chromatin, it may not be optimal to interpret alignments. Genrich has an alternative analysis mode for ATAC-seq in which it creates intervals centered on transposase cut sites. The remainder of the peak-calling process (calculating pileups and significance values) is identical to the default analysis mode. Note that the interval lengths (not the fragment lengths) are used to sum the total sequence information for the calculation of control/background pileup values.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
266
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
267 -------------------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
268
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
269 **Inputs**
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
270
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
271 -------------------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
272
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
273 Genrich analyzes alignment files in SAM/BAM format. SAM files must have a header.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
274 SAM/BAM files for multiple replicates can be specified, comma-separated (or space-separated, in quotes).
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
275 Multiple SAM/BAM files for a single replicate should be combined in advance via samtools merge.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
276 The SAM/BAM files must be sorted by queryname (via samtools sort -n).
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
277
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
278
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
279 -----------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
280
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
281 **Outputs**
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
282
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
283 -----------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
284
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
285 As indicated, the output file is in ENCODE narrowPeak format. Here are details of the fields:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
286 * 1. chrom Name of the chromosome
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
287 * 2. chromStart Starting position of the peak (0-based)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
288 * 3. chromEnd Ending position of the peak (not inclusive)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
289 * 4. name peak_N, where N is the 0-based count
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
290 * 5. score Average AUC (total AUC / bp) × 1000, rounded to the nearest int (max. 1000)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
291 * 6. strand . (no orientation)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
292 * 7. signalValue Total area under the curve (AUC)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
293 * 8. pValue Summit -log10(p-value)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
294 * 9. qValue Summit -log10(q-value), or -1 if not available (e.g. with -p)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
295 * 10. peak Summit position (0-based offset from chromStart): the midpoint of the peak interval with the highest significance (the longest interval in case of ties)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
296
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
297 Example:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
298 chr1 894446 894988 peak_10 402 . 217.824936 4.344683 1.946031 317
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
299 chr1 895834 896167 peak_11 343 . 114.331093 4.344683 1.946031 90
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
300
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
301 Optional files
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
302
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
303 -c Input SAM/BAM file(s) for control sample(s)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
304
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
305 Alignment files for control samples (e.g. input DNA) can be specified, although this is not strictly required.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
306 SAM/BAM files for multiple replicates can be listed, comma-separated (or space-separated, in quotes) and in the same order as the experimental files. Missing control files should be indicated with null.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
307
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
308 -f Output bedgraph-ish file for p/q values
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
309
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
310 With a single replicate, this log file lists experimental/control pileup values, p- and q-values, and significance (*) for each interval.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
311
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
312 Example:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
313 chr1 894435 894436 33.000000 2.477916 3.183460 1.208321
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
314 chr1 894436 894442 34.000000 2.477916 3.231466 1.241843
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
315 chr1 894442 894446 35.000000 2.477916 3.278469 1.274561
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
316 chr1 894446 894447 36.000000 2.477916 3.324516 1.306471 *
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
317 chr1 894447 894450 39.000000 2.477916 3.457329 1.398035 *
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
318 chr1 894450 894451 40.000000 2.477916 3.499948 1.427253 *
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
319 chr1 894451 894460 41.000000 2.477916 3.541798 1.455938 *
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
320
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
321 With multiple replicates, this log file lists p-values of each replicate, combined p-value, q-value, and significance for each interval.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
322 Note that this file (as well as the -k file, below) is called "bedgraph-ish" because it contains multiple dataValue fields, which isn't strictly allowed in the bedGraph format. However, a simple application of awk can produce the desired bedgraph files for visualization purposes (see this awk reference for a guide to printing specific fields of input records).
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
323 When peak-calling is skipped (-X), the significance column is not produced.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
324
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
325 -k Output bedgraph-ish file for pileups and p-values
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
326
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
327 For each replicate, sequentially, this file lists a header line (# experimental file: <name>; control file: <name>), followed by experimental/control pileups and a p-value for each interval. This is the way to examine pileup values with multiple replicates, since the -f log file does not supply them in that case.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
328
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
329 -b Output BED file for reads/fragments/intervals
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
330
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
331 This is an unsorted BED file of the reads/fragments/intervals analyzed. The 4th column gives the read name, number of valid alignments, 'E'xperimental or 'C'ontrol, and sample number (0-based), e.g. SRR5427886.59_2_E_0.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
332
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
333 -R Output file for PCR duplicates (only with -r)
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
334
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
335 This log file lists the header of each read/fragment classified as a PCR duplicate, followed by the alignment, the header of the read/fragment it matched, and the alignment type.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
336
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
337 Example:
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
338 SRR5427886.5958 chr4:185201876-185201975 SRR5427886.4688 paired
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
339 SRR5427886.1826 chr12:34372610,+;chr1:91852878,- SRR5427886.2040 discordant
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
340 SRR5427886.10866 chr14:53438632,+ SRR5427886.4746 single
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
341
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
342 The duplicates from multiple input files are separated by a comment line listing the next filename, such as # experimental file #0: SRR5427886.bam.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
343 This file can be used to filter the original SAM/BAM file, using a simple script such as getReads.py, for example.
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
344
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
345
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
346 --------------------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
347
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
348 **More Information**
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
349
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
350 --------------------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
351
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
352 See the excellent `Genrich documentation`_
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
353
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
354 .. _`Genrich documentation`: https://github.com/jsh58/Genrich
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
355
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
356
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
357 --------------------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
358
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
359 **Galaxy Wrapper Development**
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
360
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
361 --------------------
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
362
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
363 Author: Florian Heyl <heylf@informatik.uni-freiburg.de>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
364
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
365
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
366 ]]></help>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
367 <citations>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
368 <citation type="bibtex">
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
369 @misc{genrich,
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
370 title = {Genrich},
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
371 url = {https://github.com/jsh58/Genrich},
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
372 urldate = {2019-07-15},
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
373 author = {John M. Gaspar},
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
374 year = {2018},
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
375 }
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
376 </citation>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
377 </citations>
48c5ff6b11fb planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba
iuc
parents:
diff changeset
378 </tool>