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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2018.4">
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3 <description> - Extract reads from reference</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime feature-classifier extract-reads --i-sequences=$isequences --p-r-primer="$prprimer" --p-f-primer="$pfprimer"
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9
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10 #if $ptrunclen:
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11 --p-trunc-len=$ptrunclen
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12 #end if
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13
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14 #if str($cmdconfig) != 'None':
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15 --cmd-config=$cmdconfig
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16 #end if
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17
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18 #if $ptrimleft:
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19 --p-trim-left=$ptrimleft
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20 #end if
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21 --o-reads=oreads
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22 #if $pidentity:
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23 --p-identity=$pidentity
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24 #end if
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25 ;
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26 cp oreads.qza $oreads;
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27 ]]></command>
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28 <inputs>
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29 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] [required]" name="isequences" optional="False" type="data"/>
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30 <param label="--p-f-primer: forward primer sequence [required]" name="pfprimer" optional="False" type="text"/>
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31 <param label="--p-r-primer: reverse primer sequence [required]" name="prprimer" optional="False" type="text"/>
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32 <param label="--p-trunc-len: read is cut to trunc_len if trunc_len is positive. Applied before trim_left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
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33 <param label="--p-trim-left: trim_left nucleotides are removed from the 5' end if trim_left is positive. Applied after trunc_len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
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34 <param label="--p-identity: minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>
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35 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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36 </inputs>
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37 <outputs>
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38 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/>
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39 </outputs>
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40 <help><![CDATA[
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41 Extract reads from reference
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42 -----------------------------
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43
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44 Extract sequencing-like reads from a reference database.
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45
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46 Parameters
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47 ----------
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48 sequences : FeatureData[Sequence]
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49
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50 f_primer : Str
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51 forward primer sequence
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52 r_primer : Str
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53 reverse primer sequence
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54 trunc_len : Int, optional
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55 read is cut to trunc_len if trunc_len is positive. Applied before
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56 trim_left.
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57 trim_left : Int, optional
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58 trim_left nucleotides are removed from the 5' end if trim_left is
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59 positive. Applied after trunc_len.
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60 identity : Float, optional
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61 minimum combined primer match identity threshold.
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62
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63 Returns
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64 -------
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65 reads : FeatureData[Sequence]
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66 ]]>
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67 </help>
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68 <macros>
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69 <import>qiime_citation.xml</import>
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70 </macros>
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71 <expand macro="qiime_citation" />
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72 </tool>
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