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comparison methylation_analysis/methylation_extractor.xml @ 4:282edadee017 draft

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author fcaramia
date Mon, 03 Dec 2012 18:26:25 -0500
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1 <tool id="methyation_extractor_tool" name="Methylation Extractor" version="0.7.6">
2 <description>: extracts the methylation information for individual cytosine</description>
3 <requirements>
4 <requirement type="package" version="0.1.16">samtools</requirement>
5 <requirement type="package" version="0.12.7">bowtie2</requirement>
6 <requirement type="package" version="0.7.6">bismark</requirement>
7 </requirements>
8 <command interpreter="perl">
9
10 methylation_extractor_wrapper.pl
11
12
13 "GENOME::${genome.fields.path}"
14
15
16 #if str($no_overlap) == "ON":
17 "OPTION::--no_overlap"
18 #end if
19
20 #if str($ending) == "single":
21 "ENDING::-s"
22 #else
23 "ENDING::-p"
24 #end if
25
26 #if str($report) == "ON":
27 "OPTION::--report"
28 #end if
29
30 "OPTION::--bedGraph"
31
32 "OPTION::--counts"
33
34
35 "OUTPUT::$output"
36 "SUMMARY::$summary"
37
38 "BAMFILE::$bamfile"
39
40
41 </command>
42 <inputs>
43
44 <param name="genome" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
45 <options from_data_table="bismark_indexes">
46 <filter type="sort_by" column="2"/>
47 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
48 </options>
49 </param>
50
51 <param name="bamfile" type="data" format="bam" label="Bam file: bismark output" />
52
53 <param name="ending" type="select" label="ending" help="" optional="true">
54 <option value="single" >single-end</option>
55 <option value="paired" selected="true">paired-end</option>
56 </param>
57
58 <param name="no_overlap" type="select" label="no-overlap" help="" optional="true">
59 <option value="ON" selected="true">ON</option>
60 <option value="OFF">OFF</option>
61 </param>
62
63 <param name="report" type="select" label="Report" help="" optional="true">
64 <option value="ON" selected="true">ON</option>
65 <option value="OFF">OFF</option>
66 </param>
67
68 </inputs>
69 <outputs>
70 <data format="bedgraph" name="output" label="${tool.name} on ${on_string}">
71 <actions>
72 <action type="metadata" name="dbkey">
73 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
74 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
75 <filter type="param_value" ref="genome" column="0"/>
76 </option>
77 </action>
78 </actions>
79 </data>
80 <data name="summary" format="txt" label="${tool.name} summary" />
81 </outputs>
82 <help>
83 |
84
85 **Reference**
86
87 http://www.bioinformatics.babraham.ac.uk/projects/bismark/
88
89 -----
90
91 **What it does**
92
93
94
95 The script reads in a bisulfite read alignment results file
96 produced by the Bismark bisulfite mapper (BAM file) and extracts the methylation
97 informationfor individual cytosines. This information is found in the methylation
98 call field which can contain the following characters:
99
100 ::
101
102 ~~~ X for methylated C in CHG context (was protected) ~~~
103
104 ~~~ x for not methylated C CHG (was converted) ~~~
105
106 ~~~ H for methylated C in CHH context (was protected) ~~~
107
108 ~~~ h for not methylated C in CHH context (was converted) ~~~
109
110 ~~~ Z for methylated C in CpG context (was protected) ~~~
111
112 ~~~ z for not methylated C in CpG context (was converted) ~~~
113
114 ~~~ . for any bases not involving cytosines ~~~
115
116
117
118 -----
119
120 **Required Parameters**
121
122 ::
123
124 -s/--single-end Input file(s) are Bismark result file(s) generated from single-end
125 read data. Specifying either --single-end or --paired-end is
126 mandatory.
127
128 -p/--paired-end Input file(s) are Bismark result file(s) generated from paired-end
129 read data. Specifying either --paired-end or --single-end is
130 mandatory.
131
132 --no_overlap For paired-end reads it is theoretically possible that read_1 and
133 read_2 overlap. This option avoids scoring overlapping methylation
134 calls twice (only methylation calls of read 1 are used for in the process
135 since read 1 has historically higher quality basecalls than read 2).
136 Whilst this option removes a bias towards more methylation calls
137 in the center of sequenced fragments it may de facto remove a sizable
138 proportion of the data. This option is highly recommended for paired-end
139 data.
140
141 --report Prints out a short methylation summary as well as the paramaters used to run
142 this script.
143
144
145 -----
146
147 **Default Parameters**
148
149 ::
150
151 --bedGraph After finishing the methylation extraction, the methylation output is written into a
152 sorted bedGraph file that reports the position of a given cytosine and its methylation
153 state (in %, seem details below). The methylation extractor output is temporarily split up into
154 temporary files, one per chromosome (written into the current directory or folder
155 specified with -o/--output); these temp files are then used for sorting and deleted
156 afterwards. By default, only cytosines in CpG context will be sorted. The option
157 '--CX_context' may be used to report all cyosines irrespective of sequence context
158 (this will take MUCH longer!).
159
160
161
162 </help>
163 </tool>
164
165