annotate MethylDackel.xml @ 4:b327b539ec58 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 2953c88908606f4f22b3987bc4ba29bdb4c30479
author bgruening
date Sun, 12 Mar 2017 06:15:57 -0400
parents f112bf3dd5ff
children 906db57d5d65
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
1 <tool id="pileometh" name="MethylDackel" version="0.2.1">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
2 <description>A tool for processing bisulfite sequencing alignments</description>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
3 <requirements>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
4 <requirement type="package" version="0.2.1">methyldackel</requirement>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
5 </requirements>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
6 <stdio>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
7 <!-- Anything other than zero is an error -->
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
8 <exit_code range="1:" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
9 <exit_code range=":-1" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
10 <!-- In case the return code has not been set propery check stderr too -->
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
11 <regex match="Error:" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
12 <regex match="Exception:" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
13 </stdio>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
14 <version_command><![CDATA[MethylDackel --version]]></version_command>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
15 <command><![CDATA[
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
16 #if $reference_source.reference_source_selector == "cached":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
17 ln -s $reference_source.ref_file.fields.path reference.fasta &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
18 #else:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
19 ln -s $reference_source.ref_file reference.fasta &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
20 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
21
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
22 MethylDackel
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
23 $main_task.task
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
24
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
25 #if $main_task.task == "extract":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
26 -o output
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
27 $main_task.mergeContext
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
28 #if str($main_task.OT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
29 --OT $main_task.OT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
30 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
31 #if str($main_task.OB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
32 --OB $main_task.OB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
33 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
34 #if str($main_task.CTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
35 --CTOT $main_task.CTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
36 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
37 #if str($main_task.CTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
38 --CTOB $main_task.CTOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
39 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
40 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
41
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
42 #if $advanced_options.options=="yes":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
43 #if $advanced_options.mbias_regionString:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
44 -r $advanced_options.mbias_regionString
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
45 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
46 $advanced_options.keepDupes
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
47 $advanced_options.keepSingleton
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
48 $advanced_options.keepDiscordant
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
49 -q $advanced_options.min_mapq
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
50 -p $advanced_options.min_phred
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
51 -D $advanced_options.max_pbdepth
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
52 #if $main_task.task == "extract":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
53 -d $advanced_options.min_pbdepth
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
54 --ignoreFlags $advanced_options.ignoreFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
55 --requireFlags $advanced_options.requireFlags
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
56 $advanced_options.fraction
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
57 $advanced_options.counts
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
58 $advanced_options.methylKit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
59 $advanced_options.logit
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
60 #if str($advanced_options.nOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
61 --nOT $advanced_options.nOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
62 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
63 #if str($advanced_options.nOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
64 --nOB $advanced_options.nOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
65 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
66 #if str($advanced_options.nCTOT).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
67 --nCTOT $advanced_options.nCTOT
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
68 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
69 #if str($advanced_options.nCTOB).strip() != "":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
70 --nCTOB $advanced_options.nCTOB
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
71 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
72 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
73 $advanced_options.CHG
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
74 $advanced_options.CHH
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
75 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
76
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
77 reference.fasta
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
78
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
79 $input_sortedAlignBAM
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
80
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
81 #if $main_task.task == "mbias":
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
82 out_mbias &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
83 touch out_mbias_OT.svg &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
84 touch out_mbias_OB.svg &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
85 touch out_mbias_CTOT.svg &&
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
86 touch out_mbias_CTOB.svg
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
87 #end if
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
88 ]]></command>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
89 <inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
90 <conditional name="reference_source">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
91 <param name="reference_source_selector" type="select" label="Load reference genome from">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
92 <option value="cached">Local cache</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
93 <option value="history">History</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
94 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
95 <when value="cached">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
96 <param name="ref_file" type="select" label="Using reference genome" help="Reference sequence">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
97 <options from_data_table="all_fasta"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
98 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
99 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
100 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
101 <when value="history">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
102 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
103 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
104 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
105
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
106 <param name="input_sortedAlignBAM" multiple="False" type="data" format="bam" label="sorted_alignments.bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
107 <conditional name="main_task">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
108 <param name="task" type="select" label="What do you want to do?" >
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
109 <option value="extract">Extract methylation metrics from an alignment file in BAM/CRAM format</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
110 <option value="mbias">Determine the position-dependent methylation bias in a dataset, producing diagnostic SVG images</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
111 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
112 <when value="extract">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
113 <param name="mergeContext" type="boolean" checked="false" truevalue="--mergeContext" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
114 label="Merge per-Cytosine metrics from CpG and CHG contexts into per-CPG or per-CHG metrics" help="(--mergeContext)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
115 <param name="OT" type="text" value="" label="Original top strand bounds (comma-separated, no spaces)"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
116 help="Inclusion bounds for methylation calls from reads/pairs
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
117 origination from the original top strand. Suggested values can
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
118 be obtained from the MBias program. Each integer represents a
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
119 1-based position on a read. For example --OT A,B,C,D
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
120 translates to, 'Include calls at positions from A through B
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
121 on read #1 and C through D on read #2'. If a 0 is used a any
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
122 position then that is translated to mean start/end of the
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
123 alignment, as appropriate. For example, --OT 5,0,0,0 would
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
124 include all but the first 4 bases on read #1. Users are
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
125 strongly advised to consult a methylation bias plot, for
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
126 example by using the MBias program." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
127 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
128 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
129 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
130 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
131 <when value="mbias"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
132 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
133 <conditional name="advanced_options">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
134 <param name="options" type="select" label="Advanced options">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
135 <option value="">Hide advanced options</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
136 <option value="yes">Display advanced options</option>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
137 </param>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
138 <when value="yes">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
139 <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
140 <param name="keepDupes" type="boolean" checked="false" truevalue="--keepDupes" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
141 label="By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
142 <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
143 label="By default, if only one read in a pair aligns (a singleton) then it's ignored." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
144 <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
145 label="By default, paired-end alignments with the properly-paired bit unset in the FLAG field are ignored. Note that the definition of concordant and discordant is based on your aligner settings." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
146 <param name="min_mapq" type="integer" value="10" label="Minimum MAPQ threshold to include an alignment (default 10)"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
147 <param name="min_phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
148 <param name="max_pbdepth" type="integer" value="2000" label="Maximum per-base depth (default 2000)"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
149 <param name="min_pbdepth" type="integer" value="1" min="1" label="Minimum per-base depth"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
150 help="Minimum per-base dpeth for reporting output. If you use --mergeContext (above), then this applies to the merged CpG/CHG (default 1). (-d)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
151
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
152 <param name="ignoreFlags" type="integer" value="3840" label="Ignore certain alignments"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
153 help="By deault, any alignment marked as secondary (bit 0x100), failing QC (bit 0x200), a PCR/optical duplicate (0x400) or supplemental (0x800) is ignored. This equates to a value of 0xF00 or 3840 in decimal. If you would like to change that, you can specify a new value here." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
154 <param name="requireFlags" type="integer" value="0" label="Require alignment flags"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
155 help="Require each alignment to have all bits in this value present, or else the alignment is ignored. This is equivalent to the -f option in samtools. The default is 0, which includes all alignments." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
156
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
157 <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
158 label="Extract fractional methylation (only) at each position. This is mutually exclusive with --counts, --logit, and --methylKit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
159 <param name="counts" type="boolean" checked="false" truevalue="--counts" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
160 label="Extract base counts (only) at each position. This is mutually exclusive with --fraction, --logit, and --methylKit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
161 <param name="logit" type="boolean" checked="false" truevalue="--logit" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
162 label="Extract logit(M/(M+U)) (only) at each position. This is mutually exclusive with --counts, --fraction, and --methylKit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
163 <param name="methylKit" type="boolean" checked="false" truevalue="--methylKit" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
164 label="Output in the format required by methylKit. This is mutually exclusive with --counts, --fraction, and --logit" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
165
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
166 <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
167 label="Additional output file with CHG methylation metrics" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
168 <param name="CHH" type="boolean" checked="false" truevalue="--CHH" falsevalue=""
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
169 label="Additional output file with CHH methylation metrics" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
170
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
171 <param name="nOT" type="text" value="" label="Original top strand absolute bounds (comma-separated, no spaces)"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
172 help="Like --OT, but always exclude INT bases from a given end
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
173 from inclusion,regardless of the length of an alignment. This
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
174 is useful in cases where reads may have already been trimmed
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
175 to different lengths, but still none-the-less contain a
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
176 certain length bias at one or more ends." />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
177 <param name="nOB" type="text" value="" label="Original bottom strand absolute bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
178 <param name="nCTOT" type="text" value="" label="Complementary to the original bottom strand absolute bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
179 <param name="nCTOB" type="text" value="" label="Complementary to the original bottom strand absolute bounds (comma-separated, no spaces)" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
180 </when>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
181 <when value=""/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
182 </conditional>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
183 </inputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
184 <outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
185 <data name="outFileExtractCpG" format="bedgraph" from_work_dir="output_CpG.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
186 label="${tool.name} on ${on_string}">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
187 <filter>main_task['task'] == "extract"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
188 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
189 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
190 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
191 <filter>not advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
192 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
193 <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
194 label="${tool.name} on ${on_string} (logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
195 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
196 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
197 <data name="outFileExtractCpGMethylKit" format="text" from_work_dir="output_CpG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
198 label="${tool.name} on ${on_string} (MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
199 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
200 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
201 <data name="outFileExtractCpGCounts" format="bedgraph" from_work_dir="output_CpG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
202 label="${tool.name} on ${on_string} (counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
203 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
204 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
205 <data name="outFileExtractCpGFraction" format="bedgraph" from_work_dir="output_CpG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
206 label="${tool.name} on ${on_string} (fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
207 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
208 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
209 <data name="outFileExtractCHG" format="bedgraph" from_work_dir="output_CHG.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
210 label="${tool.name} on ${on_string} (CHG)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
211 <filter>main_task['task'] == 'extract'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
212 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
213 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
214 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
215 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
216 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
217 <filter>not advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
218 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
219 <data name="outFileExtractCHGLogit" format="bedgraph" from_work_dir="output_CHG.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
220 label="${tool.name} on ${on_string} (CHG logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
221 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
222 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
223 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
224 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
225 <data name="outFileExtractCHGMethylKit" format="text" from_work_dir="output_CHG.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
226 label="${tool.name} on ${on_string} (CHG MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
227 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
228 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
229 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
230 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
231 <data name="outFileExtractCHGCounts" format="bedgraph" from_work_dir="output_CHG.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
232 label="${tool.name} on ${on_string} (CHG counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
233 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
234 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
235 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
236 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
237 <data name="outFileExtractCHGFraction" format="bedgraph" from_work_dir="output_CHG.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
238 label="${tool.name} on ${on_string} (CHG fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
239 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
240 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
241 <filter>advanced_options['CHG']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
242 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
243 <data name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
244 label="${tool.name} on ${on_string} (CHH)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
245 <filter>main_task['task'] == 'extract'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
246 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
247 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
248 <filter>not advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
249 <filter>not advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
250 <filter>not advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
251 <filter>not advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
252 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
253 <data name="outFileExtractCHHLogit" format="bedgraph" from_work_dir="output_CHH.logit.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
254 label="${tool.name} on ${on_string} (CHH logit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
255 <filter>main_task['task'] == "extract" and advanced_options['logit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
256 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
257 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
258 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
259 <data name="outFileExtractCHHMethylKit" format="text" from_work_dir="output_CHH.methylKit"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
260 label="${tool.name} on ${on_string} (CHH MethylKit)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
261 <filter>main_task['task'] == "extract" and advanced_options['methylKit']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
262 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
263 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
264 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
265 <data name="outFileExtractCHHCounts" format="bedgraph" from_work_dir="output_CHH.counts.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
266 label="${tool.name} on ${on_string} (CHH counts)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
267 <filter>main_task['task'] == "extract" and advanced_options['counts']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
268 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
269 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
270 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
271 <data name="outFileExtractCHHFraction" format="bedgraph" from_work_dir="output_CHH.meth.bedGraph"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
272 label="${tool.name} on ${on_string} (CHH fraction)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
273 <filter>main_task['task'] == "extract" and advanced_options['fraction']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
274 <filter>advanced_options['options'] == "yes"</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
275 <filter>advanced_options['CHH']</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
276 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
277 <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
278 label="${tool.name} on ${on_string} (methylation bias, original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
279 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
280 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
281 <data name="outFileMbiasCpGOB" format="svg" from_work_dir="out_mbias_OB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
282 label="${tool.name} on ${on_string} (methylation bias, original bottom strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
283 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
284 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
285 <data name="outFileMbiasCpGCTOT" format="svg" from_work_dir="out_mbias_CTOT.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
286 label="${tool.name} on ${on_string} (methylation bias, complementary to the original top strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
287 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
288 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
289 <data name="outFileMbiasCpGCTOB" format="svg" from_work_dir="out_mbias_CTOB.svg"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
290 label="${tool.name} on ${on_string} (methylation bias, complementary to the original bottom strand)">
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
291 <filter>main_task['task'] == 'mbias'</filter>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
292 </data>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
293 </outputs>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
294 <tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
295 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
296 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
297 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
298 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
299 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
300 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
301 <param name="mergeContext" value="false"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
302 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
303 <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
304 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
305 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
306 <param name="task" value="mbias" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
307 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
308 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
309 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
310 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
311 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
312 <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
313 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
314 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
315 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
316 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
317 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
318 <param name="CHH" value="True"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
319 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
320 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
321 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
322 <param name="mergeContext" value="false"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
323 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
324 <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
325 <output name="outFileExtractCHH" file="test_2.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
326 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
327 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
328 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
329 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
330 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
331 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
332 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
333 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
334 <param name="fraction" value="true" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
335 <output name="outFileExtractCpGFraction" file="test_3.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
336 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
337 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
338 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
339 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
340 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
341 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
342 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
343 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
344 <param name="logit" value="true" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
345 <output name="outFileExtractCpGLogit" file="test_4.bedGraph" ftype="bedgraph" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
346 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
347 <test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
348 <param name="task" value="extract" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
349 <param name="min_mapq" value="2" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
350 <param name="reference_source_selector" value="history" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
351 <param name="ref_file" value="cg100.fa" ftype="fasta" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
352 <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
353 <param name="options" value="yes"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
354 <param name="methylKit" value="true" />
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
355 <output name="outFileExtractCpGMethylKit" file="test_5.methylKit" ftype="text" compare="diff"/>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
356 </test>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
357 </tests>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
358 <help><![CDATA[
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
359
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
360 .. image:: $PATH_TO_IMAGES/MethylDackelLogo.png
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
361 :align: left
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
362
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
363 **What it does**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
364
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
365 MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
366
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
367 By default, MethylDackel will only calculate metrics for Cytosines in a CpG context, but metrics for those in CHG and CHH contexts are supported as well.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
368
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
369 **Methylation context**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
370
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
371 MethylDackel groups all Cytosines into one of three sequence contexts: CpG, CHG, and CHH. Here, H is the IUPAC ambiguity code for any nucleotide other than G. If an N is encountered in the reference sequence, then the context will be assigned to CHG or CHH, as appropriate (e.g., CNG would be categorized as in a CHG context and CNC as in a CHH context). If a Cytosine is close enough to the end of a chromosome/contig such that its context can't be inferred, then it is categorized as CHH (e.g., a Cytosine as the last base of a chromosome is considered as being in a CHH context).
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
372
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
373
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
374 **Output information**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
375
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
376 If no methylation can be found, the output will be empty.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
377
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
378 Otherwise a variant of bedGraph that's similar to the "coverage" file is produced. In short, each line consists of 6 tab separated columns:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
379
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
380 1. The chromosome/contig/scaffold name
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
381 2. The start coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
382 3. The end coordinate
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
383 4. The methylation percentage rounded to an integer
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
384 5. The number of alignments/pairs reporting methylated bases
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
385 6. The number of alignments/pairs reporting unmethylated bases
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
386
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
387 All coordinates are 0-based half open, which conforms to the bedGraph definition. When paired-end reads are aligned, it can often occur that their alignments overlap. In such cases, MethylDackel will not count both reads of the pair in its output, as doing so would lead to incorrect downstream statistical results.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
388
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
389 An example of the output is below::
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
390
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
391 #track type="bedGraph" description="SRR1182519.sorted CpG methylation levels"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
392 #1 25115 25116 100 3 0
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
393 #1 29336 29337 50 1 1
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
394
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
395 Note the header line, which starts with "track". The "description" field is used as a label in programs such as IGV. Each of the subsequent lines describe single Cytosines, the 25116th and 29337th base on chromosome 1, respectively. The first position has 3 alignments (or pairs of alignments) indicating methylation and 0 indicating unmethylation (100% methylation) and the second position has 1 alignment each supporting methylation and unmethylation (50% methylation).
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
396
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
397 **Per-CpG/CHG metrics**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
398
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
399 In many circumstances, it's desireable for metrics from individual Cytosines in a CpG to be merged, producing per-CpG metrics rather than per-Cytosine metrics. This can be accomplished with the **Merge per-Cytosine** parameter. If this is used, then this output::
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
400
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
401 #track type="bedGraph" description="SRR1182519.sorted CpG methylation levels"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
402 #1 25114 25115 100 2 1
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
403 #1 25115 25116 100 3 0
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
404
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
405 is changed to this::
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
406
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
407 #track type="bedGraph" description="SRR1182519.sorted merged CpG methylation levels"
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
408 #1 25114 25116 100 5 1
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
409
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
410 This also works for CHG-level metrics. If bedGraph files containing per-Cytosine metrics already exist, they can be converted to instead contain per-CpG/CHG metrics with MethylDackel mergeContext.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
411
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
412 **Methylation bias plotting and correction**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
413
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
414 In an ideal experiment, we expect that the probability of observing a methylated C is constant across the length of any given read. In practice, however, there are often increases/decreases in observed methylation rate at the ends of reads and/or more global changes. These are termed methylation bias and including such regions in the extracted methylation metrics will result in noisier and less accurate data. For this reason, users are strongly encouraged to make a methylation bias plot.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
415
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
416 That command will create a methylation bias (mbias for short) plot for each of the strands for which there are valid alignments.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
417 The resulting mbias graphs are in SVG format and can be viewed in most modern web browsers:
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
418
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
419 .. image:: $PATH_TO_IMAGES/example.svg
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
420
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
421
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
422 If you have paired-end data, both reads in the pair will be shown separately, as is the case above. The program will suggest regions for inclusion ("--OT 2,0,0,98" above) and mark them on the plot, if applicable. The format of this output is described in MethylDackel extract -h. These suggestions should not be accepted blindly; users are strongly encouraged to have a look for themselves and tweak the actual bounds as appropriate. The lines indicate the average methylation percentage at a given position and the shaded regions the 99.9% confidence interval around it. This is useful in gauging how many methylation calls a given position has relative to its neighbors. Note the spike in methylation at the end of read #2 and the corresponding dip at the beginning of read #1. This is common and these regions can be ignored with the suggested trimming bounds. Note also that the numbers refer to the first and last base that should be included during methylation extraction, not the last and first base to ignore!.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
423
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
424 **Excluding low-coverage regions**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
425
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
426 If your downstream analysis requires an absolute minimum coverage (here, defined as the number of methylation calls kept after filtering for MAPQ, phred score, etc.), you can use the `--minDepth` option to achieve this. By default, `MethylDackel extract` will output all methylation metrics as long as the coverage is at least 1. If you use `--minDepth 10`, then only sites covered at least 10x will be output. This works in conjunction with the `--mergeContext` option, above. So if you request per-CpG context output (i.e., with `--mergeContext`) and `--minDepth 10` then only CpGs with a minimum coverage of 10 will be output.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
427
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
428 **Logit, fraction, and counts only output**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
429
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
430 The standard output described above can be modified if you supply the `--fraction`, `--counts`, or `--logit` options to `MethylDackel extract`.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
431
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
432 The `--fraction` option essentially produces the first 4 columns of the standard output described above. The only other difference is that the range of the 4th column is now between 0 and 1, instead of 0 and 100. Instead of producing a file ending simply in `.bedGraph`, one ending in `.meth.bedGraph` will instead be produced.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
433
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
434 The `--counts` option produces the first three columns of the standard output followed by a column of total coverage counts. This last column is equivalent to the sum of the 5th and 6th columns of the standard output. The resulting file ends in `.counts.bedGraph` rather than simply `.bedGraph`.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
435
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
436 The `--logit` option produces the first three columns of the standard output followed by the logit transformed methylation fraction. The logit transformation is log(Methylation fraction/(1-Methylation fraction)). Note that log uses base e. Logit transformed methylation values range between +/- infinity, rather than [0,1]. The resulting file ends in `.logit.bedGraph` rather than simply `.bedGraph`.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
437
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
438 Note that these options may be combined with `--mergeContext`. However, `MethylDackel mergeContext` can not be used after the fact to combine these.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
439
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
440 **methylKit-compatible output**
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
441
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
442 methylKit has its own format, which can be produced with the `--methylKit` option. Merging Cs into CpGs or CHGs is forbidden in this format. Likewise, this option is mutually exclusive with `--logit` et al.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
443
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
444
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
445 -----
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
446
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
447 **MethylDackel** is a Free and Open Source Software, see more details on the MethylDackel_ Website.
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
448
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
449 .. _MethylDackel: https://github.com/dpryan79/MethylDackel
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
450 ]]></help>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
451 <citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
452 </citations>
f112bf3dd5ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 5468fb89708be679e4e580074734e671f60a9648
bgruening
parents:
diff changeset
453 </tool>