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1 <tool id="confindr" name="confindr" label="Detect sequence contamination using rMLST" version="0.1.3">
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2 <requirements>
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3 <requirement type="package" version="0.4.3">confindr</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 mkdir in out;
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7 #if $jobtype.select == "fastq_single"
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8 perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name;
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9 #else if $jobtype.select == "fastq_fr"
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10 perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name;
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11 perl $__tool_directory__/makein.pl in $jobtype.fastq2 $jobtype.fastq2.name;
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12 #else if $jobtype.select == "fastq_pair"
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13 perl $__tool_directory__/makein.pl in $jobtype.coll.forward $jobtype.coll.forward.name;
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14 perl $__tool_directory__/makein.pl in $jobtype.coll.reverse $jobtype.coll.reverse.name;
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15 #end if
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16 confindr.py -i in -o out
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17 #if $options.select=="advanced"
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18 #if $options.threads
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19 -t $options.threads
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20 #end if
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21 #if $options.quality
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22 -q $options.quality
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23 #end if
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24 #if $options.basecut
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25 -b $options.basecut
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26 #end if
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27 #if $options.basefrac
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28 -bf $options.basefrac
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29 #end if
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30 #if $options.datatype
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31 -dt $options.datatype
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32 #end if
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33 #else if $options.select=="basic"
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34 -t \${GALAXY_SLOTS:-1}
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35 #end if
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36 ]]></command>
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37 <inputs>
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38 <conditional name="jobtype">
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39 <param name="select" type="select" label="Select Input">
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40 <option value="fastq_single">Single FASTQ</option>
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41 <option value="fastq_fr">Forward and Reverse FASTQ</option>
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42 <option value="fastq_pair">Paired FASTQ Collection</option>
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43 </param>
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44 <when value="fastq_single">
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45 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
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46 </when>
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47 <when value="fastq_fr">
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48 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" />
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49 <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" />
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50 </when>
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51 <when value="fastq_pair">
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52 <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
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53 </when>
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54 </conditional>
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55 <conditional name="options">
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56 <param name="select" type="select" label="Basic or Advanced Settings">
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57 <option value="basic">Basic</option>
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58 <option value="advanced">Advanced</option>
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59 </param>
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60 <when value="advanced">
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61 <param name="threads" optional="true" type="integer" label="Number of threads (Default=all)" value=""/>
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62 <param name="quality" optional="true" type="integer" label="Base quality needed to support a multiple allele call (Default=20)" value=""/>
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63 <param name="basecut" optional="true" type="integer" label="Number of bases necessary to support a multiple allele call (Default=2)" value=""/>
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64 <param name="basefrac" optional="true" type="float" label="Fraction of bases necessary to support a multiple call." value="">
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65 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
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66 </param>
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67 <param name="datatype" type="select" label="Data Type">
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68 <option value="Illumina">Illumina</option>
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69 <option value="Nanopore">Nanopore</option>
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70 <option value="auto">auto</option>
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71 </param>
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72 </when>
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73 <when value="basic">
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74 </when>
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75 </conditional>
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76 </inputs>
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77 <outputs>
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78 <data name="output" type="data" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="out/confindr_report.csv" />
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79 </outputs>
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80 <help><![CDATA[
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81 ]]></help>
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82 <citations>
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83 <citation type="bibtex">
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84 @misc{githubconfindr,
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85 author = {Low,Andrew},
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86 year = {2018},
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87 title = {confindr},
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88 publisher = {GitHub},
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89 journal = {GitHub repository},
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90 url = {https://github.com/lowandrew/ConFindr},
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91 }</citation>
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92 </citations>
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93 </tool>
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