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annotate trimmer.xml @ 0:c824894e0827 draft

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author nick
date Tue, 01 Dec 2015 21:11:51 -0500
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1 <tool id="sequence_content_trimmer" version="0.1" name="Sequence Content Trimmer">
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2 <description>trim reads based on certain bases</description>
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3 <command interpreter="python">
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4 trimmer.py $input1
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5 #if $paired.is_paired:
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6 $input2 $output1 $output2
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7 #if ('fasta' in $input1.extension and 'fastq' in $input2.extension) or ('fastq' in $input1.extension and 'fasta' in $input2.extension)
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8 --error 'Both input files must be either fastq or fasta (no mixing the two).'
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9 #end if
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10 #end if
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11 #if $input1.extension == 'fastq' or $input1.extension == 'fastqsanger' or $input1.extension == 'fastqillumina' or $input1.extension == 'fastqsolexa'
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12 -f fastq
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13 #elif $input1.extension == 'fasta'
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14 -f fasta
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15 #else
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16 -f $input1.extension
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17 #end if
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18 -b $bases -t $thres -w $win_len $invert
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19 #if $min_len.has_min_len:
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20 -m $min_len.value
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21 #end if
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22 #if not $paired.is_paired:
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23 &gt; $output1
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24 #end if
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25 </command>
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26 <inputs>
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27 <conditional name="paired">
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28 <param name="is_paired" type="select" label="Paired reads?">
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29 <option value="" selected="True">Unpaired</option>
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30 <option value="true">Paired</option>
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31 </param>
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32 <when value="true">
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33 <param name="input1" type="data" format="fasta,fastq" label="Input reads (mate 1)"/>
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34 <param name="input2" type="data" format="fasta,fastq" label="Input reads (mate 2)"/>
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35 </when>
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36 <when value="">
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37 <param name="input1" type="data" format="fasta,fastq" label="Input reads"/>
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38 </when>
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39 </conditional>
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40 <param name="bases" type="text" value="N" label="Bases to filter on"/>
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41 <param name="thres" type="float" value="0.5" min="0" max="1" label="Frequency threshold" help="trim when the frequency of filter bases (or non-filter bases, if inverting) exceeds this value."/>
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42 <param name="win_len" type="integer" value="10" min="1" label="Size of the window"/>
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43 <param name="invert" type="boolean" truevalue="--invert" falsevalue="" checked="False" label="Invert filter bases" help="Trim when the frequency of bases NOT in the &quot;filter bases&quot; list exceeds the threshold."/>
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44 <conditional name="min_len">
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45 <param name="has_min_len" type="boolean" truevalue="true" falsevalue="" checked="False" label="Set a minimum read length"/>
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46 <when value="true">
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47 <param name="value" type="integer" value="10" min="0" label="Minimum read length" help="Reads trimmed to less than this length will be omitted from the output. Pairs will be preserved: both must exceed this threshold to be kept."/>
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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="output1" format_source="input1"/>
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53 <data name="output2" format_source="input2">
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54 <filter>paired['is_paired']</filter>
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55 </data>
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56 </outputs>
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57
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58 <help>
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59
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60 .. class:: infomark
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61
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62 **What it does**
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63
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64 This tool trims the 3' ends of reads based on the presence of the given bases. For instance, trim when N's are encountered or when the GC content exceeds a certain frequency.
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65
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66
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67 .. class:: infomark
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68
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69 **Input**
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70
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71 The inputs can be in the following formats: fasta, fastq, fastqsanger, fastqillumina, and fastqsolexa. Both must be either a fasta or fastq type (no mixing fastq and fasta).
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72
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73 </help>
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74
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75 </tool>