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1 <tool id="confindr" name="ConFindr" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="0.7.4">confindr</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 ## Copy and optionally uncompress reads ##
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7 #if $reads.reads_select == 'collection'
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8 #set forward=$reads.coll.forward
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9 #set reverse=$reads.coll.reverse
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10 #set name=$reads.coll.name.replace(' ', '_')
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11 #else
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12 #set name=$forward.name.split('_')[0]
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13 #end if
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14 mkdir ./${name}
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15 #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
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16 && cp $forward ./${name}/${name}_R1.fastq.gz
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17 #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
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18 && tar -vxjOf $forward > ./${name}/${name}_R1.fastq
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19 #else
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20 && cp $forward ./${name}/${name}_R1.fastq
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21 #end if
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22 #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
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23 && cp $reverse ./${name}/${name}_R2.fastq.gz
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24 #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
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25 && tar -vxjOf $reverse > ./${name}/${name}_R2.fastq
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26 #else
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27 && cp $reverse ./${name}/${name}_R2.fastq
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28 #end if
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29 ## !!! confindr in single-threaded mode; race condition bugs in multiple threads !!! ##
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30 && confindr.py -i ./${name} -o ./output -t 1
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31 && cat ./output/confindr_log.txt
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32 && ls -lah ./output/confindr_report.csv
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33
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34 ]]></command>
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35 <inputs>
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36 <conditional name="reads">
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37 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
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38 <option value="collection">Paired collection from your history</option>
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39 <option value="history">Two FASTQ datasets from your history</option>
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40 </param>
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41 <when value="collection">
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42 <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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43 </when>
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44 <when value="history">
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45 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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46 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data format="csv" name="contam_report" label="Contamination Report" from_work_dir="./output/confindr_report.csv" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="reads_select" value="collection" />
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56 <param name="coll">
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57 <collection type="paired">
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58 <element name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz" />
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59 <element name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz" />
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60 </collection>
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61 </param>
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62 <output name="contam_report" value="confindr_report.csv" />
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63 </test>
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64 <test>
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65 <param name="reads_select" value="history" />
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66 <param name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz"/>
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67 <param name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz"/>
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68 <output name="contam_report" value="confindr_report_2.csv" />
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69 </test>
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70 <test>
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71 <param name="reads_select" value="history" />
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72 <param name="forward" value="example_R1.fastq.bz2" ftype="fastqsanger.bz2"/>
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73 <param name="reverse" value="example_R2.fastq.bz2" ftype="fastqsanger.bz2"/>
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74 <output name="contam_report" value="confindr_report_2.csv" />
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 ConFindr, a contamination screen for Illumina sequencing
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79 ]]></help>
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80 <citations>
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81 <citation type="doi">10.7717/peerj.6995</citation>
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82 <citation type="bibtex">
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83 @misc{githubConFindr,
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84 author = {LastTODO, FirstTODO},
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85 year = {TODO},
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86 title = {ConFindr},
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87 publisher = {GitHub},
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88 journal = {GitHub repository},
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89 url = {https://github.com/OLC-Bioinformatics/ConFindr},
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90 }</citation>
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91 </citations>
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92 </tool>
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