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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author simonl
date Tue, 07 Jun 2011 16:22:51 -0400
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1 <tool id="agile_wrapper" name="AGILE" version="1.0.0">
2 <description> Quickly match reads to a reference genome or sequence file</description>
3 <command interpreter="python">
4 #if $source.source_select=="database" #agile_wrapper.py 0 $source.dbkey $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
5 #else #agile_wrapper.py 1 $source.input_target $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
6 #end if# ${GALAXY_DATA_INDEX_DIR}
7 </command>
8 <inputs>
9 <conditional name="source">
10 <param name="source_select" type="select" label="Target source">
11 <option value="database">Genome Build</option>
12 <option value="input_ref">Your Upload File</option>
13 </param>
14 <when value="database">
15 <param name="dbkey" type="genomebuild" label="Genome" />
16 </when>
17 <when value="input_ref">
18 <param name="input_target" type="data" label="Reference sequence" />
19 </when>
20 </conditional>
21 <param name="input_query" type="data" format="fasta" label="Query sequences file"/>
22 <param name="max_sims" type="integer" size="15" value="7" label="Maximum number of Single Imperfect Matches (SIMs) allowed as percentage of read length (-maxSIMs, default 7)" />
23 <param name="tile_size" type="integer" size="15" value="20" label="Sets the length of tuples for creating hash table (-tileSize, default 20)" help="Usually between 11 and 20."/>
24 <param name="max_freq" type="integer" size="15" value="8" label="Maximum number of occurrences of a pattern (k-tupple) allowed (-maxFreq, default 8"/>
25 <param name="all" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output all matches? (-all, default true for MHC)"/>
26 <param name="out_type" type="select" label="Output Format (-out default pslx for MHC">
27 <option value="pslx">pslx</option>
28 <option value="psl">psl</option>
29 <option value="axt">axt</option>
30 <option value="maf">maf</option>
31 <option value="sim4">sim4</option>
32 <option value="wublast">wublast</option>
33 <option value="blast">blast</option>
34 <option value="blast8">blast8</option>
35 <option value="blast9">blast9</option>
36 </param>
37 </inputs>
38 <outputs>
39 <data name="output1" format="tabular"/>
40 </outputs>
41 <requirements>
42 <requirement type="binary">agile</requirement>
43 </requirements>
44 <help>
45
46 .. class:: warningmark
47
48 The default parameter values can be altered in the agile tool xml file
49
50 -----
51
52 **What it does**
53
54 This tool uses the **AGILE** alignment program, a faster replacement for the **BLAT** algorithm. Your reads file is searched against a genome build or another uploaded file.
55
56 -----
57
58 **Parameters**
59
60 - *Maximum Single Imperfect Matches* (**-maxSIMs**) : The number of allowable mismatches as a percentage of read length.
61
62 - *Tuple Length* (**-tileSize**) : The length of tuples for craring a hash table.
63
64 - *Maximum Frequency* (**-maxFreq**) : The maximum number of pattern occurrences allowed.
65
66 - *All Matches* (**-all**) : Output all matches satisfying the match criteria (true/false).
67
68 - *Output Format* (**-out**) : Define the output format for the match file.
69
70 -----
71
72 **Reference**
73
74 **AGILE**: Sanchit Misra, Ankit Agrawal, Wei-keng Liao, Alok Choudhary. Anatomy of a Hash-based Long Read Sequence Mapping Algorithm for Next Generation DNA Sequencing. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq648.
75
76
77 </help>
78 </tool>