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1 <tool id="map_chromosomes" name="Convert between UCSC and ensembl chromosome names" version="0.0.1">
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2 <description>chromosome representation</description>
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3 <command interpreter="perl">map_chromosomes.pl $input1 $col $delimiter ${map.fields.path} $out_file1</command>
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4 <inputs>
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5 <param format="tabular,txt" name="input1" type="data" label="this dataset"/>
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6 <param name="col" type="integer" value="1" label="Column containing chromosome ids"/>
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7 <param name="delimiter" type="select" label="Delimited by">
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8 <option value="TAB">Tab</option>
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9 <option value="SPACE">Whitespace</option>
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10 <option value="DOT">Dot</option>
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11 <option value="COMMA">Comma</option>
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12 <option value="DASH">Dash</option>
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13 <option value="UNDERSCORE">Underscore</option>
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14 <option value="PIPE">Pipe</option>
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15 </param>
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16 <param name="map" type="select" label="Select a mapping file" help="Ensure you select the correct mapping file">
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17 <options from_data_table="map_chromosomes">
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18 <filter type="sort_by" column="2"/>
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19 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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20 </options>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data name="out_file1" format="input" metadata_source="input1"/>
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25 </outputs>
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26
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27 <tests>
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28 <test>
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29 <param name="col" value="1"/>
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30 <param name="delimiter" value="TAB"/>
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31 <param name="map" value="hg19 UCSC to ensembl"/>
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32 <param name="input1" value="map_chrom_ucsc.txt" dbkey="hg19" />
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33 <output name="out_file1" file="map_chrom_ensembl.txt"/>
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34 </test>
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35 <test>
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36 <param name="col" value="1"/>
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37 <param name="delimiter" value="TAB"/>
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38 <param name="map" value="hg19 ensembl to UCSC"/>
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39 <param name="input1" value="map_chrom_ensembl.txt" dbkey="hg19" />
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40 <output name="out_file1" file="map_chrom_ucsc.txt"/>
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41 </test>
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42 </tests>
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43 <help>
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44
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45
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46 **What it does**
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47
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48 Converts a column between the UCSC and ensembl representation of chromosomes.
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49
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50 .. class:: warningmark
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51
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52 **Warning any lines containing chromosomes that don't map or are invalid will be removed**
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53
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54 -----
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55
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56 **Example 1**
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57
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58 Converting this dataset::
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59
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60 chr21 12 123
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61 chrM 45 345
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62
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63 by setting **Column** to *1*, **Delimiter** to *Tab* and **Mapping** file to *hg19 UCSC to ensembl** will produce::
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64
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65 21 12 123
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66 MT 45 345
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67
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68 -----
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69
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70 **Example 2**
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71
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72 Converting this dataset::
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73
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74 21 12 123
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75 MT 45 345
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76
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77 by setting **Column** to *1*, **Delimiter** to *Tab* and **Mapping** file to *hg19 ensembl to UCSC** will produce::
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78
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79 chr21 12 123
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80 chrM 45 345
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81
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82
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83 </help>
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84 </tool>
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