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1 <tool id="makeFasta" name="Extract IDs" force_history_refresh="True">
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2 <description>from Read Aligner output</description>
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3 <command interpreter="perl">
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4 #if $format.formatChoice == "fasta" #makeFasta.pl --input $input --genes "$genes.g" --outFormat $format.formatChoice --out $out --id $out.id --output_path $__new_file_path__
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5 #else #makeFasta.pl --input $input --genes "$genes.g" --outFormat $format.formatChoice --limit $format.limit --out $out --id $out.id --output_path $__new_file_path__
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6 #end if#
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7
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8 </command>
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9 <inputs>
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10 <param name="input" type="data" format="fasta" label="Read Aligner output file" help="Fasta file"/>
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11 <conditional name="genes">
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12 <param name="choice" type="select" label="Choose IDs by">
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13 <option value="index">ID Index File</option>
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14 <option value="number" selected="true">Text Box</option>
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15 </param>
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16 <when value="index">
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17 <param name="indices" type="data" format="tabular" label="ID Index"/>
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18 <param name="g" type="select" multiple="true" accept_default="true" label="ID" >
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19 <options from_dataset="indices">
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20 <column name="name" index="0"/>
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21 <column name="value" index="0"/>
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22 </options>
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23 </param>
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24 </when>
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25 <when value="number">
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26 <param name="g" type="text" format="txt" size="200" value="" label="IDs" help="Enter identifiers separated by a comma">
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27 <validator type="empty_field" />
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28 </param>
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29 </when>
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30 </conditional>
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31 <conditional name="format">
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32 <param name="formatChoice" type="select" label="Choose output format">
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33 <option value="fasta" selected="true">Fasta</option>
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34 <option value="align">Tabular Alignment</option>
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35 <option value="both">Both</option>
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36 </param>
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37 <when value="align">
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38 <param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50">
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39 <validator type="in_range" min="50" message="Please enter a value greater than 50"/>
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40 </param>
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41 </when>
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42 <when value="both">
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43 <param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50">
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44 <validator type="in_range" min="50" message="Please enter a value greater than 50"/>
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45 </param>
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46 </when>
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47 <when value="fasta">
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48 </when>
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49 </conditional>
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50 </inputs>
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51 <outputs>
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52 <data name="out" format="txt" label="Extract IDs"/>
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53 </outputs>
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54 <help>
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55 .. class:: infomark
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56
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57 **What it does**
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58
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59 Splits the fasta pyReadAligner output in to individual files per selected ID.
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60
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61 To select IDs by text box
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62
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63 - Enter identifiers separated by a comma e.g RDN37-1,RPL7A,SNR17A.
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64
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65 To select IDs by ID index file
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66
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67 - Provide a file of data type indexfile (use pencil icon to edit data type)
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68 - The index file should contain all possible IDs in the first column
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69 - Select multiple IDs by holding Shift or Ctrl keys
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70
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71 Output formats
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72
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73 - Fasta - Output reads and reference sequence in fasta format
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74 - Alignment tab - Format output to show read sequences aligned to reference sequence
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75 - Both - Output both of the formats above
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76
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77 </help>
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78 </tool>
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79
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