Mercurial > repos > drosofff > ged_bowtie
comparison sRbowtie_wrapper.xml @ 0:05ae11c21834 draft
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author | drosofff |
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date | Sun, 11 May 2014 18:16:18 -0400 |
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-1:000000000000 | 0:05ae11c21834 |
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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> |