|
16
|
1 <tool id="Bismark" name="Bismark Mapper">
|
|
|
2 <requirements>
|
|
|
3 <requirement type='package'>
|
|
|
4 Bismark
|
|
|
5 </requirement>
|
|
|
6 </requirements>
|
|
|
7 <command interpreter="bash">
|
|
|
8 bismark_wrapper.sh
|
|
|
9 ##Reference genome
|
|
|
10 ref="${indices.fields.path}"
|
|
|
11 ##Output files (SAM output, Bismark summary)
|
|
|
12 mapped=$mapped
|
|
|
13 summary=$summary
|
|
|
14 ##Temp directory
|
|
|
15 tempdir=$mapped.files_path
|
|
|
16 #if str($singlePaired.sPaired) == "single":
|
|
|
17 library=single
|
|
|
18 mate1=$singlePaired.sInput1
|
|
|
19 #if $singlePaired.sParams.sSettingsType == "full":
|
|
|
20 fullparam=true
|
|
|
21 qual=$singlePaired.sParams.qual
|
|
|
22 seedmms=$singlePaired.sParams.seedmms
|
|
|
23 seedlen=$singlePaired.sParams.seedlen
|
|
|
24 maqerr=$singlePaired.sParams.maqerr
|
|
|
25 directional=$singlePaired.sParams.non_directional
|
|
|
26 header=$singlePaired.sParams.sam_no_hd
|
|
|
27 #end if
|
|
|
28 #else:
|
|
|
29 library=paired
|
|
|
30 mate1=$singlePaired.pInput1
|
|
|
31 mate2=$singlePaired.pInput2
|
|
|
32 #if $singlePaired.pParams.pSettingsType == "full":
|
|
|
33 fullparam="true"
|
|
|
34 qual=$singlePaired.pParams.qual
|
|
|
35 seedmms=$singlePaired.pParams.seedmms
|
|
|
36 seedlen=$singlePaired.pParams.seedlen
|
|
|
37 maqerr=$singlePaired.pParams.maqerr
|
|
|
38 directional=$singlePaired.pParams.non_directional
|
|
|
39 header=$singlePaired.pParams.sam_no_hd
|
|
|
40 minins=$singlePaired.pParams.minins
|
|
|
41 maxins=$singlePaired.pParams.maxins
|
|
|
42 #end if
|
|
|
43 #end if
|
|
|
44
|
|
|
45
|
|
|
46 </command>
|
|
|
47 <inputs>
|
|
|
48 <param name="indices" type="select" label="Select a reference genome">
|
|
|
49 <options from_data_table="bismark_bs_indeces">
|
|
|
50 <filter type="sort_by" column="2" />
|
|
|
51 <validator type="no_options" message="No indexes are available" />
|
|
|
52 </options>
|
|
|
53 </param>
|
|
|
54
|
|
|
55 <conditional name="singlePaired">
|
|
|
56 <param name="sPaired" type="select" label="Is this library mate-paired?">
|
|
|
57 <option value="single">Single-end</option>
|
|
|
58 <option value="paired">Paired-end</option>
|
|
|
59 </param>
|
|
|
60 <when value="single">
|
|
|
61 <param name="sInput1" type="data" format="fastq" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
|
|
|
62 <conditional name="sParams">
|
|
|
63 <param name="sSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
|
|
|
64 <option value="preSet">Commonly used</option>
|
|
|
65 <option value="full">Full parameter list</option>
|
|
|
66 </param>
|
|
|
67 <when value="preSet" />
|
|
|
68 <when value="full">
|
|
|
69 <param name="qual" type="select" label="Select the type of FastQ qualities">
|
|
|
70 <option value="--phred33-quals">phred33-quals</option>
|
|
|
71 <option value="--phred64-quals">phred64-quals</option>
|
|
|
72 <option value="--solexa-quals">solexa-quals</option>
|
|
|
73 </param>
|
|
|
74 <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" />
|
|
|
75 <param name="seedlen" type="integer" value="28" label="The seed length" />
|
|
|
76 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" />
|
|
|
77 <param name="non_directional" type="select" label="Is the library a non-directional one?">
|
|
|
78 <option value="">No</option>
|
|
|
79 <option value="--non_directional">Yes</option>
|
|
|
80 </param>
|
|
|
81 <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?">
|
|
|
82 <option value="">No</option>
|
|
|
83 <option value="--sam-no-hd">Yes</option>
|
|
|
84 </param>
|
|
|
85 </when> <!-- full -->
|
|
|
86 </conditional> <!-- sParams -->
|
|
|
87 </when> <!-- single -->
|
|
|
88
|
|
|
89 <when value="paired">
|
|
|
90 <param name="pInput1" type="data" format="fastq" label="Forward FASTQ file" />
|
|
|
91 <param name="pInput2" type="data" format="fastq" label="Reverse FASTQ file" />
|
|
|
92
|
|
|
93 <conditional name="pParams">
|
|
|
94 <param name="pSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
|
|
|
95 <option value="preSet">Commonly used</option>
|
|
|
96 <option value="full">Full parameter list</option>
|
|
|
97 </param>
|
|
|
98 <when value="preSet" />
|
|
|
99 <when value="full">
|
|
|
100 <param name="minins" type="integer" value="0" label="The minimum insert size for valid paired-end alignments" />
|
|
|
101 <param name="maxins" type="integer" value="500" label="The maximum insert size for valid paired-end alignments" />
|
|
|
102 <param name="qual" type="select" label="Select the type of FastQ qualities">
|
|
|
103 <option value="--phred33-quals">phred33-quals</option>
|
|
|
104 <option value="--phred64-quals">phred64-quals</option>
|
|
|
105 <option value="--solexa-quals">solexa-quals</option>
|
|
|
106 </param>
|
|
|
107 <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" />
|
|
|
108 <param name="seedlen" type="integer" value="28" label="The seed length" />
|
|
|
109 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" />
|
|
|
110 <param name="non_directional" type="select" label="Is the library a non-directional one?">
|
|
|
111 <option value="">No</option>
|
|
|
112 <option value="--non_directional">Yes</option>
|
|
|
113 </param>
|
|
|
114 <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?">
|
|
|
115 <option value="">No</option>
|
|
|
116 <option value="--sam-no-hd">Yes</option>
|
|
|
117 </param>
|
|
|
118 </when> <!-- full -->
|
|
|
119 </conditional> <!-- pParams -->
|
|
|
120 </when> <!-- paired -->
|
|
|
121 </conditional> <!-- singlePaired -->
|
|
|
122
|
|
|
123
|
|
|
124 </inputs>
|
|
|
125 <outputs>
|
|
|
126 <data name="mapped" format="sam" label="Bismark Mapped Reads" />
|
|
|
127 <data name="summary" format ="txt" label="Bismark Mapping Summary" />
|
|
|
128 </outputs>
|
|
|
129 <help>
|
|
|
130 **What it does**
|
|
|
131
|
|
|
132 Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are:
|
|
|
133
|
|
|
134 - Bisulfite mapping and methylation calling in one single step
|
|
|
135
|
|
|
136 - Supports single-end and paired-end read alignments
|
|
|
137
|
|
|
138 - Supports ungapped and gapped alignments
|
|
|
139
|
|
|
140 - Alignment seed length, number of mismatches etc. are adjustable
|
|
|
141
|
|
|
142 - Output discriminates between cytosine methylation in CpG, CHG and CHH context
|
|
|
143
|
|
|
144 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
|
|
|
145
|
|
|
146 **Input formats**
|
|
|
147
|
|
|
148 Bismark accepts files in Sanger FASTQ format.
|
|
|
149
|
|
|
150 **Outputs**
|
|
|
151
|
|
|
152 The output is in SAM format, and has the following columns::
|
|
|
153
|
|
|
154 Column Description
|
|
|
155 -------- --------------------------------------------------------
|
|
|
156 1 QNAME seq-ID
|
|
|
157 2 FLAG this flag tries to take the strand a bisulfite read originated from into account (this is different from ordinary DNA alignment flags!)
|
|
|
158 3 RNAME chromosome
|
|
|
159 4 POS start position
|
|
|
160 5 MAPQ always 255
|
|
|
161 6 CIGAR
|
|
|
162 7 RNEXT
|
|
|
163 8 PNEXT
|
|
|
164 9 TLEN
|
|
|
165 10 SEQ
|
|
|
166 11 QUAL Phred33 scale
|
|
|
167 12 NM-tag edit distance to the reference
|
|
|
168 13 XX-tag base-by-base mismatches to the reference, not including indels
|
|
|
169 14 XM-tag methylation call string
|
|
|
170 15 XR-tag read conversion state for the alignment
|
|
|
171 16 XG-tag genome conversion state for the alignment
|
|
|
172
|
|
|
173 </help>
|
|
|
174 </tool>
|
|
|
175
|
