Mercurial > repos > eugen > bs_seq_test_1

comparison bismark.xml @ 16:bfda928ca5d8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author eugen
date Wed, 15 Aug 2012 09:46:54 -0400
parents
children
comparison
equal deleted inserted replaced
15:8aec1cc3b71f 16:bfda928ca5d8
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