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6
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1 <tool id="trimSequences" name="trim sequences">
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15
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2 <description>Remove the 5' and/or 3' adapters of a list of reads.</description>
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18
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6
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6 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
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7 #if $OptionFPADP.FPADP == "Yes":
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8 -5 $OptionFPADP.fivePAdaptor
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9 #end if
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10 #if $OptionTPADP.TPADP == "Yes":
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11 -3 $OptionTPADP.threePAdaptor
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12 #end if
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15
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13 -e $errors
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6
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14 $indels
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15 $noAdaptor5p $noAdaptorFile5p
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16 $noAdaptor3p $noAdaptorFile3p
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17 -o $outputFile
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18
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19 </command>
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20
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21
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22 <inputs>
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23 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
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24
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25 <conditional name="OptionFPADP">
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15
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26 <param name="FPADP" type="select" label="5' adapter">
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6
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27 <option value="Yes">Yes</option>
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28 <option value="No" selected="true">No</option>
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29 </param>
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30 <when value="Yes">
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31 <param name="fivePAdaptor" type="text" value="None" />
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32 </when>
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33 <when value="No">
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34 </when>
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35 </conditional>
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36
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37 <conditional name="OptionTPADP">
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15
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38 <param name="TPADP" type="select" label="3' adapter">
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6
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39 <option value="Yes">Yes</option>
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40 <option value="No" selected="true">No</option>
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41 </param>
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42 <when value="Yes">
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43 <param name="threePAdaptor" type="text" value="None" />
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44 </when>
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45 <when value="No">
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46 </when>
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47 </conditional>
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48
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15
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49 <param name="errors" type="integer" label="number of errors in percent" value="0" />
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6
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50 <param name="indels" type="boolean" truevalue="-d" falsevalue="" checked="false" label="indels option" help="also accept indels"/>
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15
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51 <param name="noAdaptor5p" type="boolean" truevalue="-n" falsevalue="" checked="false" label="noAdaptor 5' option" help="file name where to print sequences with no 5' adapter "/>
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52 <param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adapter "/>
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6
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53
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54 </inputs>
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55
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56 <outputs>
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18
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57 <data format="fastq" name="outputFile" label="[trim sequences] output file"/>
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58 <data name="noAdaptorFile5p" format="fastq" label="[trim sequences] noAdapter5p file">
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6
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59 <filter>noAdaptor5p</filter>
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60 </data>
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18
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61 <data name="noAdaptorFile3p" format="fastq" label="[trim sequences] noAdapter3p file">
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6
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62 <filter>noAdaptor3p</filter>
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63 </data>
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64 </outputs>
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65
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66 <help>
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18
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67 This function removes the adaptor from the 5' or 3' end of your reads. It can even recognize the adaptators which are partially present. You can specify whether you are ready to accept indels or not.
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6
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68 </help>
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15
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69 <tests>
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70 <test>
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71 <param name="inputFile" value="short_fastq.fastq" />
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72 <param name="FPADP" value="Yes"/>
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18
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73 <param name="fivePAdaptor" value="AAAA" />
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15
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74 <param name="TPADP" value="No"/>
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18
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75 <param name="errors" value="1"/>
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15
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76 <param name="indels" value="False"/>
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18
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77 <param name="noAdaptor5p" value="False"/>
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15
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78 <param name= "noAdaptor3p" value="False"/>
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18
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79 <output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
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15
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80 </test>
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81 </tests>
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6
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82 </tool>
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