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annotate fairy_sketch.xml @ 0:666cf1a9572c draft default tip

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planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
author iuc
date Sun, 12 Jan 2025 19:00:01 +0000
parents
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0
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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1 <tool id="fairy_sketch" name="Fairy sketch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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2 <description>sketching of k-mers for coverage into a hashtable</description>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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3 <macros>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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4 <import>macros.xml</import>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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5 </macros>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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6 <expand macro="requirements"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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7 <command detect_errors="exit_code">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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8 <![CDATA[
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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9
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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10 #import re
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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11
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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12 mkdir -p res &&
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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13
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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14 #if $input.is_select == "single":
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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15 #set $file = re.sub('[^\s\w\-\\.]', '_', str($reads.element_identifier))
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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16 #set $filename = $file + '.bcsp'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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17 ln -s '$reads' '$file' &&
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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18 #else if $input.is_select == 'pair':
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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19 #set $file_1 = re.sub('[^\s\w\-\\.]', '_', str($first_pairs.element_identifier))
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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20 #set $file_2 = re.sub('[^\s\w\-\\.]', '_', str($second_pairs.element_identifier))
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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21 ## Since the tool used the first inputed file to name the output file this has to be used there to cp the right file
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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22 #set $filename = $file_1 + '.paired.bcsp'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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23 ln -s '$first_pairs' '$file_1' &&
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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24 ln -s '$second_pairs' '$file_2' &&
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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25 #else
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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26 #set $file_1 = re.sub('[^\s\w\-\\.]', '_', str($paired_collection.forward.element_identifier))
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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27 #set $file_2 = re.sub('[^\s\w\-\\.]', '_', str($paired_collection.reverse.element_identifier))
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
parents:
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28 ## Since the tool used the first inputed file to name the output file this has to be used there to cp the right file
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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29 #set $filename = $file_1 + '.paired.bcsp'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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30 ln -s '$paired_collection.forward' '$file_1' &&
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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31 ln -s '$paired_collection.reverse' '$file_2' &&
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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32 #end if
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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33
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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34 fairy sketch
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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35 -t "\${GALAXY_SLOTS:-3}"
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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36 -c ${c}
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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37 -k ${k}
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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38 -d 'res'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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39 #if $input.is_select == "single":
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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40 -r '$file'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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41 #else
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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42 -1 '$file_1'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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43 -2 '$file_2'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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44 #end if
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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45 &&
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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46
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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47 cp './res/${filename}' '$output'
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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48
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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49 ]]>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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50 </command>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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51 <inputs>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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52 <conditional name="input">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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53 <param name="is_select" type="select" label="Single or paired-end reads">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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54 <option value="single">Single</option>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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55 <option value="pair">Paired</option>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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56 <option value="paired_collection">Paired collection</option>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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57 </param>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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58 <when value="single">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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59 <param argument="--reads" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input single-end reads"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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60 </when>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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61 <when value="pair">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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62 <param argument="--first_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input first paired-end reads"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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63 <param argument="--second_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input second paired-end reads"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
parents:
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64 </when>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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65 <when value="paired_collection">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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66 <param name="paired_collection" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" type="data_collection" collection_type="paired" label="Input paired collection reads"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
parents:
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67 </when>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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68 </conditional>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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69 <param argument="-c" type="integer" value="50" optional="true" label="Set the subsampling rate"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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70 <param argument="-k" type="select" label="Select k-mer size">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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71 <option value="31">31</option>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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72 <option value="21">21</option>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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73 </param>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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74 </inputs>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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75 <outputs>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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76 <data name="output" format="bcsp" label="${tool.name} on ${on_string}"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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77 </outputs>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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78 <tests>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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79 <test>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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80 <conditional name="input">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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81 <param name="is_select" value="single"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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82 <param name="reads" value="single_test.fasta.gz" ftype="fasta.gz"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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83 </conditional>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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84 <output name="output" file="single_test.fasta.gz.bcsp"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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85 </test>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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86 <test>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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87 <conditional name="input">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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88 <param name="is_select" value="pair"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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89 <param name="first_pairs" value="test_paired_1.fq.gz" ftype="fastq.gz"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
parents:
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90 <param name="second_pairs" value="test_paired_2.fq.gz" ftype="fastq.gz"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
parents:
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91 </conditional>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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92 <output name="output" file="test_paired_1.fq.gz.paired.bcsp"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
parents:
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93 </test>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
parents:
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94 <test>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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95 <conditional name="input">
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
iuc
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96 <param name="is_select" value="paired_collection"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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97 <param name="paired_collection">
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98 <collection type="paired">
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99 <element name="forward" value="test_paired_1.fq.gz" ftype="fastq.gz" />
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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100 <element name="reverse" value="test_paired_2.fq.gz" ftype="fastq.gz" />
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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101 </collection>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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102 </param>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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103 </conditional>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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104 <output name="output" file="forward.paired.bcsp"/>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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105 </test>
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106 </tests>
666cf1a9572c planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6
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107 <help>
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108 <![CDATA[
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109
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110 This tool sketch the k-mer into a hashtable which will be needed for the fairy coverage tool to create the coverage file.
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111
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112 .. class:: infomark
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113
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114 This tool can either use single-end or paired-end reads as input in multiple file formats.
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115 ]]>
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116 </help>
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117 <expand macro="citations"/>
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118 </tool>