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1 <?xml version="1.0"?>
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2 <tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0">
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3 <description>trim FASTQ using the Phred algorithm</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[seqtk trimfq
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10 #if $mode.mode_select == "quality":
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11 -q $mode.q
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12 -l $mode.l
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13 #else:
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14 -b $mode.b
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15 -e $mode.e
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16 #end if
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17 $in_file
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18 > $default]]></command>
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19 <inputs>
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20 <expand macro="in_faq"/>
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21 <conditional name="mode">
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22 <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
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23 <option value="quality">Quality</option>
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24 <option value="position">Length/Position</option>
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25 </param>
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26 <when value="quality">
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27 <param label="error rate threshold" help="(-q)" name="q" type="float" value="0.05"/>
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28 <param label="maximally trim down to INT bp" help="(-l)" name="l" type="integer" value="30"/>
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29 </when>
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30 <when value="position">
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31 <param label="trim INT bp from left" help="(-b)" name="b" type="integer" value="0"/>
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32 <param label="trim INT bp from right" help="(-e)" name="e" type="integer" value="0"/>
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33 </when>
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34 </conditional>
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35 </inputs>
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36 <outputs>
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37 <data format_source="in_file" hidden="false" name="default" label="$in_file.name trimmed"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="in_file" value="seqtk_trimfq.fq"/>
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42 <param name="mode_select" value="quality"/>
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43 <param name="q" value="0.05"/>
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44 <param name="l" value="30"/>
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45 <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
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46 </test>
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47 <test>
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48 <param name="in_file" value="seqtk_trimfq.fq"/>
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49 <param name="mode_select" value="position"/>
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50 <param name="b" value="5"/>
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51 <param name="e" value="5"/>
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52 <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56 **What it does**
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57
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58 Trim a fastq file based on Phred scores, or by length
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59
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60 @ATTRIBUTION@
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61 ]]></help>
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62 </tool>
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