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author drosofff
date Tue, 13 May 2014 03:14:45 -0400
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1 <tool id="sRbowtie" name="GED bowtie" version="1.0.0">
2 <description>small RNA oriented</description>
3 <requirements><requirement type='package'>bowtie</requirement></requirements>
4 <parallelism method="basic"></parallelism>
5 <command interpreter="python"> sRbowtie_wrapper.py $input
6 $method
7 $v_mismatches
8 $output_type
9 $refGenomeSource.genomeSource
10 ## the very source of the index (indexed or fasta file)
11 #if $refGenomeSource.genomeSource == "history":
12 $refGenomeSource.ownFile
13 #else:
14 $refGenomeSource.index
15 #end if
16 ##
17 $output
18 $aligned
19 $unaligned
20 </command>
21 <inputs>
22 <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files"/>
23 <!-- which method will be used -->
24 <param name="method" type="select" label="What kind of matching do you want to do?" help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand">
25 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
26 <option value="unique">Match unique mappers on DNA reference index</option>
27 <option value="multiple" selected="true">Match on DNA, multiple mappers randomly matched at a single position</option>
28 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
29 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
30 <option value="a_option">Match and report all valid alignments</option>
31 </param>
32
33 <!-- END of which method will be used -->
34
35 <param name="v_mismatches" type="select" label="Number of mismatches allowed" help="specify the -v bowtie option">
36 <option value="0">0</option>
37 <option value="1" selected="true">1</option>
38 <option value="2">2</option>
39 <option value="3">3</option>
40 </param>
41
42
43 <!-- nouvel index in dev below -->
44 <conditional name="refGenomeSource">
45 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
46 <option value="indexed">Use a built-in index</option>
47 <option value="history">Use one from the history</option>
48 </param>
49
50 <when value="indexed">
51 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
52 <options from_data_table="ged_bowtie_indexes"/>
53 </param>
54 </when>
55 <when value="history">
56 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
57 </when>
58 </conditional>
59 <!-- nouvel index input FIN -->
60 <param name="output_type" type="select" label="Select output format" help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below">
61 <option value="tabular" select="true">tabular</option>
62 <option value="sam">sam</option>
63 <option value="bam">bam</option>
64 </param>
65
66 <param name="additional_fasta" type="select" label="additional fasta output" help="to get aligned and unaligned reads in fasta format">
67 <option value="No" select="true">No</option>
68 <option value="al">aligned</option>
69 <option value="unal">unaligned</option>
70 <option value="al_and_unal">both aligned and unaligned</option>
71 </param>
72
73 </inputs>
74 <outputs>
75 <data format="tabular" name="output" label="Bowtie Output">
76 <change_format>
77 <when input="output_type" value="sam" format="sam" />
78 <when input="output_type" value="bam" format="bam" />
79 </change_format>
80 </data>
81
82 <data format="fasta" name="aligned" label="Matched reads">
83 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
84 </data>
85 <data format="fasta" name="unaligned" label ="Unmatched reads">
86 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
87 </data>
88 </outputs>
89
90 <help>
91
92 **What it does**
93
94 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
95
96 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
97
98 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
99
100 However, this useful Bowtie wrapper tool only takes as inputs FASTQ files.
101
102 Our sRbowtie wrapper is intented to work specifically with short reads FASTA inputs and to serve downstream small RNA sequencing analyses
103
104 ------
105
106 **OPTIONS**
107
108 .. class:: infomark
109
110 This script uses Bowtie to match reads on a reference index.
111
112 Depending on the type of matching, different bowtie options are used:
113
114 **Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
115
116 Match on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches, the polarity column is suppressed in the bowtie tabular report:
117
118 *-v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8*
119
120 **Match unique mappers on DNA reference index**
121
122 Match ONLY unique mappers on DNA reference index
123
124 *-v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8*
125
126 Note that using this option with -v values other than 0 is questionnable...
127
128 **Match on DNA, multiple mappers randomly matched at a single position**
129
130 Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
131
132 *-v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8*
133
134 **Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
135
136 Match with highest speed, not guaranteeing best hit for speed gain:
137
138 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
139
140
141 -----
142
143 **Input formats**
144
145 .. class:: warningmark
146
147 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
148
149 -----
150
151 **OUTPUTS**
152
153 If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::
154
155 Column Description
156 -------- --------------------------------------------------------
157 1 FastaID fasta identifier
158 2 polarity + or - depending whether the match was reported on the forward or reverse strand
159 3 target name of the matched target
160 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
161 5 Seq sequence of the matched Read
162
163 If you choose SAM, you will get the output in unordered SAM format.
164
165 .. class:: warningmark
166
167 if you choose BAM, the output will be in sorted BAM format.
168 To be viewable in Trackster, several condition must be fulfilled:
169
170 .. class:: infomark
171
172 Reads must have been matched to a FULL genome whose chromosome names are compatible with Trackster genome indexes
173
174 .. class:: infomark
175
176 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
177
178 Please contact the GED galaxy team is your reference genome is not referenced properly in GED galaxy
179
180 **Optionnal matched and unmatched fasta reads can be obtained, for further annotations**
181
182 </help>
183 </tool>