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1 <tool id="reads_subsampler" name="Subsample FASTQ Reads" version="1.0.0" python_template_version="3.5">
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2 <description>to reduce excess genomic coverage</description>
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3 <requirements>
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4 <requirement type="package" version="3.7">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #if $reads.reads_select == 'collection'
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8 python3 ${__tool_directory__}/subsamplr.py '$reads.coll.forward' '$reads.coll.reverse' '$downsampled.forward' '$downsampled.reverse' $coverage $genome_size '$seed'
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9 #else
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10 #if $reverse
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11 python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed'
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12 #else
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13 python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed'
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14 #end if
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15 #end if
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16 ]]></command>
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17 <inputs>
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18 <conditional name="reads">
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19 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
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20 <option value="collection">Paired collection from your history</option>
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21 <option value="history">Two FASTQ datasets from your history representing paired reads, forward and reverse</option>
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22 <option value="single">One FASTQ dataset representing single-end sequencing</option>
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23 </param>
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24 <when value="collection">
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25 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
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26 </when>
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27 <when value="history">
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28 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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29 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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30 </when>
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31 <when value="single">
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32 <param label="Reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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33 </when>
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34 </conditional>
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35 <param name="coverage" type="integer" label="Maximum Coverage" value="200" />
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36 <param name="genome_size" type="select" label="Assumed Genome Size">
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37 <option value="4500000">Salmonella, E. Coli (4500000)</option>
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38 <option value="2700000">Listeria (2700000)</option>
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39 <option value="29900">SARS-CoV-2 (29900)</option>
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40 </param>
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41 <param name="seed" type="text" value="ed2b99d842cddc1ac81d7c01a0bf0555" label="Random seed (you don't have to change this)"/>
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42 </inputs>
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43 <outputs>
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44 <data name="forward_out" label="${reads.forward}.downsampled" format_source="forward">
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45 <filter>reads['reads_select'] == "history" or reads['reads_select'] == "single"</filter>
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46 </data>
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47 <data name="reverse_out" label="$reads.forward}.downsampled" format_source="reverse">
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48 <filter>reads['reads_select'] == "history"</filter>
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49 </data>
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50 <collection name="downsampled" type="paired" label="${reads.coll.name}" structured_like="reads|coll" format_source="reads|coll">
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51 <filter>reads['reads_select'] == "collection"</filter>
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52 <data name="forward" label="${reads.coll.forward.name}.downsampled" format_source="reads.coll.forward" />
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53 <data name="reverse" label="${reads.coll.reverse.name}.downsampled" format_source="reads.coll.reverse" />
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54 </collection>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <conditional name="reads">
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59 <param name="reads_select" value="collection" />
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60 <param name="coll">
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61 <collection type="paired">
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62 <element name="forward" value="forward.fastq" ftype="fastqsanger" />
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63 <element name="reverse" value="reverse.fastq" ftype="fastqsanger" />
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64 </collection>
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65 </param>
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66 </conditional>
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67 <param name="coverage" value="20" />
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68 <param name="genome_size" value="29900" />
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69 <output_collection name="downsampled" type="paired">
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70 <element name="forward" file="forward_out.fastq" />
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71 <element name="reverse" file="reverse_out.fastq" />
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72 </output_collection>
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73 </test>
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74 <test>
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75 <conditional name="reads">
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76 <param name="reads_select" value="history" />
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77 <param name="forward" value="forward.fastq" />
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78 <param name="reverse" value="reverse.fastq" />
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79 </conditional>
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80 <param name="coverage" value="20" />
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81 <param name="genome_size" value="29900" />
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82 <output name="forward_out" value="forward_out.fastq" />
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83 <output name="reverse_out" value="reverse_out.fastq" />
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84 </test>
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85 <test>
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86 <conditional name="reads">
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87 <param name="reads_select" value="history" />
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88 <param name="forward" value="forward.fastq.gz" />
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89 <param name="reverse" value="reverse.fastq.gz" />
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90 </conditional>
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91 <param name="coverage" value="20" />
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92 <param name="genome_size" value="29900" />
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93 <output name="forward_out" value="forward_out.fastq.gz" decompress="true" />
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94 <output name="reverse_out" value="reverse_out.fastq.gz" decompress="true" />
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95 </test>
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96 <test>
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97 <conditional name="reads">
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98 <param name="reads_select" value="history" />
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99 <param name="forward" value="forward.fastq.bz2" />
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100 <param name="reverse" value="reverse.fastq.bz2" />
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101 </conditional>
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102 <param name="coverage" value="20" />
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103 <param name="genome_size" value="29900" />
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104 <output name="forward_out" value="forward_out.fastq.bz2" decompress="true" />
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105 <output name="reverse_out" value="reverse_out.fastq.bz2" decompress="true" />
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 Randomly subsample single or paired-end FASTQ reads to target a certain genomic coverage depth.
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110 ]]></help>
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111 <citations />
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112 </tool> |
