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1 <tool id="Paired_fastQ_trimmer" name="Paired FastQ QC-Trimmer" >
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2 <description></description>
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3 <requirements>
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4 <requirement type='package' version='1.92'>perl_module_threads</requirement>
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5 <requirement type='package' version='1.46'>perl_module_threads_shared</requirement>
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6 <requirement type='package' version='3.02'>perl_module_Thread_Queue</requirement>
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7
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8 </requirements>
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9 <command interpreter="perl">Paired_fastQ_trimmer.pl -v 0 -i "$inputforward" -q "$trimq" -n "$readnames" -s "$style" -o $output1 -F $output3 -S $side -m $minlength
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10 #if $IsPaired.paired=="true":
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11 -I $inputreverse
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12 -O $output2
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13 #end if
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14 </command>
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15
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16 <inputs>
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17 <param name="trimq" value="30" type="integer" label="Quality Threshold (phred)" />
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18 <param name="minlength" value="18" type="integer" label="Discard Reads shorter than this value as failed" />
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19 <param name="readnames" value="@" type="text" label="First (eg 5) characters of the read names" />
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20 <param name="style" type="select" label="Trimming Style to use" >
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21 <option value='simple'>Simple 1bp-window trimming</option>
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22 <option value='bwa'>BWA-Style trimming (bwa -q param)</option>
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23 </param>
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24 <param name="side" type="select" label="Which side of the reads should be trimmed" >
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25 <option value='b'>Both 5' and 3'</option>
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26 <option value='3'>3' only</option>
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27 <option value='5'>5' only</option>
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28 </param>
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29 <conditional name="IsPaired">
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30 <param name="paired" type="select" label="Is the data paired-end?">
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31 <option value="false">Single-end</option>
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32 <option value="true">Paired-end</option>
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33 </param>
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34 <when value='true'>
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35 <param format="fastqsanger" name="inputforward" type="data" label="FASTQ file with Forward Reads" />
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36 <param name='inputreverse' type='data' format='fastqsanger' label='FASTQ file with Reverse Reads' />
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37 </when>
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38 <when value='false'>
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39 <param format="fastqsanger" name="inputforward" type="data" label="FASTQ to trim" />
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40 </when>
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41 </conditional>
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42 </inputs>
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43
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44 <outputs>
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45 <data format='fastqsanger' name="output1" label="${tool.name} on ${on_string}: Forward reads"/>
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46 <data format='fastqsanger' name='output2' label="${tool.name} on ${on_string}: Reverse reads">
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47 <filter>(IsPaired['paired'] == 'true')</filter>
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48 </data>
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49 <data format='fastqsanger' name='output3' label="${tool.name} on ${on_string}: Removed read pairs" />
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50 </outputs>
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51 <help>
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52
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53 **What it does**
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54
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55 This tool trims FASTQ files based on quality score. It handles paired-end data in a single step, supporting simple trimming and BWA-style trimming.
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56
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57
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58 </help>
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3
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59 <citations>
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60 <citation type="doi">10.1111/cge.12470</citation>
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61 </citations>
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0
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62 </tool>
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