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1 <tool id="rmap_wrapper" name="RMAP" version="1.0.0">
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2 <description>for Solexa Short Reads Alignment</description>
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3 <requirements>
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4 <requirement type="package" version="2.05">rmap</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 #if $trim.choice=="No":
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8 rmap_wrapper.py $database $input_seq 0 $align_len $mismatch $output1
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9 #else:
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10 rmap_wrapper.py $database $input_seq $trim.read_len $align_len $mismatch $output1
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11 #end if
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12 </command>
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13 <inputs>
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14 <param name="database" type="select" display="radio" label="Target database">
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15 <options from_file="faseq.loc">
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16 <column name="name" index="0"/>
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17 <column name="value" index="0"/>
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18 </options>
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19 </param>
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20 <param name="input_seq" type="data" format="fasta" label="Sequence file"/>
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21 <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed" />
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22 <param name="mismatch" type="select" label="Number of mismatches allowed (-m)">
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23 <option value="0">0</option>
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24 <option value="1">1</option>
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25 <option value="3">3</option>
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26 <option value="5">5</option>
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27 </param>
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28 <conditional name="trim">
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29 <param name="choice" type="select" label="To trim the reads">
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30 <option value="No">No</option>
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31 <option value="Yes">Yes</option>
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32 </param>
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33 <when value="No">
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34 </when>
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35 <when value="Yes">
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36 <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)"/>
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37 </when>
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38 </conditional>
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39 </inputs>
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40 <outputs>
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41 <data name="output1" format="bed"/>
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42 </outputs>
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43 <!--
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44 <tests>
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45 <test>
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46 <param name="database" value="/galaxy/data/faseq/test" />
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47 <param name="input_seq" value="rmap_wrapper_test1.fasta" ftype="fasta"/>
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48 <param name="read_len" value="36" />
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49 <param name="align_len" value="36" />
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50 <param name="mismatch" value="3" />
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51 <output name="output1" file="rmap_wrapper_test1.bed"/>
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52 </test>
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53 </tests>
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54 -->
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55 <help>
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56
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57 .. class:: warningmark
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58
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59 RMAP was developed for **Solexa** reads.
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60
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61 .. class:: infomark
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62
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63 **TIP**. The tool will guess the length of the reads, however, if you select to trim the reads, the *Reads length* must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end.
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64
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65 -----
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66
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67 **What it does**
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68
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69 This tool runs **rmap** (for more information, please see the reference below), mapping Solexa reads onto a genome build.
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70
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71 -----
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72
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73 **Parameters**
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74
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75 - *Minimal Length of a Hit* (**-h**) : this is the seed length or the minimal exact match length
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76 - *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment
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77 - *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end.
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78
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79 -----
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80
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81 **Reference**
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82
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83 **RMAP** is developed by Dr. Andrew D Smith and Dr. Zhenyu Xuan at the Cold Spring Harbor Laboratory. Please see http://rulai.cshl.edu/rmap/
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84
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85 </help>
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86 </tool>
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