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annotate seqtk_trimfq.xml @ 16:48a51c72f5e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:58:58 -0400
parents 16f2535c08bf
children 069c8f0695ee
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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[
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10 seqtk trimfq
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11 #if $mode.mode_select == "quality":
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12 -q $mode.q
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13 -l $mode.l
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14 #else:
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15 -b $mode.b
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16 -e $mode.e
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17 #end if
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18 '$in_file'
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19 @CONDITIONAL_GZIP_OUT@
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20 ]]></command>
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21 <inputs>
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22 <expand macro="in_faq"/>
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23 <conditional name="mode">
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24 <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
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25 <option value="quality">Quality</option>
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26 <option value="position">Length/Position</option>
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27 </param>
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28 <when value="quality">
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29 <param argument="-q" type="float" value="0.05" label="Error rate threshold" />
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30 <param argument="-l" type="integer" value="30" label="Maximally trim down to INT bp" />
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31 </when>
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32 <when value="position">
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33 <param argument="-b" type="integer" value="0" label="Trim INT bp from left" />
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34 <param argument="-e" type="integer" value="0" label="Trim INT bp from right" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="default" format_source="in_file" label="$in_file.name trimmed"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
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44 <param name="mode_select" value="quality"/>
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45 <param name="q" value="0.05"/>
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46 <param name="l" value="30"/>
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47 <output name="default" file="seqtk_trimfq_default.fq" ftype="fastqsanger"/>
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48 </test>
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49 <test>
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50 <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
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51 <param name="mode_select" value="position"/>
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52 <param name="b" value="5"/>
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53 <param name="e" value="5"/>
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54 <output name="default" file="seqtk_trimfq_be.fq" ftype="fastqsanger"/>
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55 </test>
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56 <test>
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57 <param name="in_file" value="seqtk_trimfq.fq.gz" ftype="fastqsanger.gz"/>
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58 <param name="mode_select" value="position"/>
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59 <param name="b" value="5"/>
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60 <param name="e" value="5"/>
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61 <output name="default" file="seqtk_trimfq_be.fq.gz" ftype="fastqsanger.gz"/>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 **What it does**
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66
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67 Trim a fastq file based on Phred scores, or by length
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68
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69 @ATTRIBUTION@
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70 ]]></help>
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71 <expand macro="citation" />
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72 </tool>