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comparison sRbowtie/sRbowtie.xml @ 0:324c3142ca0f draft

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author drosofff
date Mon, 19 May 2014 17:33:06 -0400
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1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.0.0">
2 <description>for FASTA small reads</description>
3 <requirements>
4 <requirement type='package'>bowtie</requirement>
5 </requirements>
6 <parallelism method="basic"></parallelism>
7 <command interpreter="python"> sRbowtie.py $input
8 $method
9 $v_mismatches
10 $output_type
11 $refGenomeSource.genomeSource
12 ## the very source of the index (indexed or fasta file)
13 #if $refGenomeSource.genomeSource == "history":
14 $refGenomeSource.ownFile
15 #else:
16 $refGenomeSource.index.fields.path
17 #end if
18 $output
19 $aligned
20 $unaligned
21 \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
22 </command>
23 <inputs>
24 <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files"/>
25 <!-- which method will be used -->
26 <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">
27 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
28 <option value="unique">Match unique mappers on DNA reference index</option>
29 <option value="multiple" selected="true">Match on DNA, multiple mappers randomly matched at a single position</option>
30 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
31 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
32 <option value="a_option">Match and report all valid alignments</option>
33 </param>
34 <!-- END of which method will be used -->
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 <!-- bowtie index selection -->
42 <conditional name="refGenomeSource">
43 <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">
44 <option value="indexed">Use a built-in index</option>
45 <option value="history">Use one from the history</option>
46 </param>
47 <when value="indexed">
48 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
49 <options from_data_table="bowtie_indexes">
50 <!-- <filter type="sort_by" column="2" />
51 <validator type="no_options" message="No indexes are available" /> -->
52 </options>
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 <!-- END bowtie index selection -->
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 <param name="additional_fasta" type="select" label="additional fasta output" help="to get aligned and unaligned reads in fasta format">
66 <option value="No" select="true">No</option>
67 <option value="al">aligned</option>
68 <option value="unal">unaligned</option>
69 <option value="al_and_unal">both aligned and unaligned</option>
70 </param>
71 </inputs>
72 <outputs>
73 <data format="tabular" name="output" label="Bowtie Output">
74 <change_format>
75 <when input="output_type" value="sam" format="sam" />
76 <when input="output_type" value="bam" format="bam" />
77 </change_format>
78 </data>
79 <data format="fasta" name="aligned" label="Matched reads">
80 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
81 </data>
82 <data format="fasta" name="unaligned" label ="Unmatched reads">
83 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
84 </data>
85 </outputs>
86
87 <test>
88 <param name="genomeSource" value="indexed" />
89 <param name="index" value="/home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49" />
90 <param name="method" value="multiple" />
91 <param name="input" ftype="fasta" value="sRbowtie.fa" />
92 <param name="v_mismatches" value="1" />
93 <param name="output_type" value="tabular" />
94 <output name="output" ftype="tabular" value="sRbowtie.out" />
95 <output name="aligned" value="None" />
96 <output name="unaligned" value="None" />
97 </test>
98
99 <help>
100
101 **What it does**
102
103 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.
104
105 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
106
107 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
108
109 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
110
111 The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)
112
113 ------
114
115 **OPTIONS**
116
117 .. class:: infomark
118
119 This script uses Bowtie to match reads on a reference index.
120
121 Depending on the type of matching, different bowtie options are used:
122
123 **Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
124
125 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:
126
127 *-v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8*
128
129 **Match unique mappers on DNA reference index**
130
131 Match ONLY unique mappers on DNA reference index
132
133 *-v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8*
134
135 Note that using this option with -v values other than 0 is questionnable...
136
137 **Match on DNA, multiple mappers randomly matched at a single position**
138
139 Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
140
141 *-v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8*
142
143 **Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
144
145 Match with highest speed, not guaranteeing best hit for speed gain:
146
147 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
148
149
150 -----
151
152 **Input formats**
153
154 .. class:: warningmark
155
156 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
157
158 -----
159
160 **OUTPUTS**
161
162 If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::
163
164 Column Description
165 -------- --------------------------------------------------------
166 1 FastaID fasta identifier
167 2 polarity + or - depending whether the match was reported on the forward or reverse strand
168 3 target name of the matched target
169 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
170 5 Seq sequence of the matched Read
171
172 If you choose SAM, you will get the output in unordered SAM format.
173
174 .. class:: warningmark
175
176 if you choose BAM, the output will be in sorted BAM format.
177 To be viewable in Trackster, several condition must be fulfilled:
178
179 .. class:: infomark
180
181 Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes
182
183 .. class:: infomark
184
185 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
186
187 Please contact the Galaxy instance administrator if your genome is not referenced
188
189 **Matched and unmatched fasta reads can be retrieved, for further analyses**
190
191 </help>
192 </tool>