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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 15:46:41 -0400
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916a6f334881 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="agile_wrapper" name="AGILE" version="1.0.0">
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2 <description> Quickly match reads to a reference genome or sequence file</description>
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3 <command interpreter="python">
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4 #if $source.source_select=="database" #agile_wrapper.py 0 $source.dbkey $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
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5 #else #agile_wrapper.py 1 $source.input_target $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
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6 #end if# ${GALAXY_DATA_INDEX_DIR}
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7 </command>
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8 <inputs>
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9 <conditional name="source">
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10 <param name="source_select" type="select" label="Target source">
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11 <option value="database">Genome Build</option>
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12 <option value="input_ref">Your Upload File</option>
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13 </param>
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14 <when value="database">
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15 <param name="dbkey" type="genomebuild" label="Genome" />
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16 </when>
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17 <when value="input_ref">
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18 <param name="input_target" type="data" label="Reference sequence" />
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19 </when>
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20 </conditional>
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21 <param name="input_query" type="data" format="fasta" label="Query sequences file"/>
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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)" />
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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."/>
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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"/>
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25 <param name="all" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output all matches? (-all, default true for MHC)"/>
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26 <param name="out_type" type="select" label="Output Format (-out default pslx for MHC">
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27 <option value="pslx">pslx</option>
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28 <option value="psl">psl</option>
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29 <option value="axt">axt</option>
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30 <option value="maf">maf</option>
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31 <option value="sim4">sim4</option>
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32 <option value="wublast">wublast</option>
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33 <option value="blast">blast</option>
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34 <option value="blast8">blast8</option>
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35 <option value="blast9">blast9</option>
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36 </param>
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37 </inputs>
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38 <outputs>
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39 <data name="output1" format="tabular"/>
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40 </outputs>
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41 <requirements>
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42 <requirement type="binary">agile</requirement>
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43 </requirements>
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44 <help>
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45
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46 .. class:: warningmark
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47
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48 The default parameter values can be altered in the agile tool xml file
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49
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50 -----
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51
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52 **What it does**
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53
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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.
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55
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56 -----
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57
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58 **Parameters**
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59
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60 - *Maximum Single Imperfect Matches* (**-maxSIMs**) : The number of allowable mismatches as a percentage of read length.
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61
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62 - *Tuple Length* (**-tileSize**) : The length of tuples for craring a hash table.
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63
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64 - *Maximum Frequency* (**-maxFreq**) : The maximum number of pattern occurrences allowed.
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65
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66 - *All Matches* (**-all**) : Output all matches satisfying the match criteria (true/false).
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67
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68 - *Output Format* (**-out**) : Define the output format for the match file.
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69
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70 -----
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71
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72 **Reference**
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73
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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.
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75
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76
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77 </help>
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78 </tool>