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1 <tool id="ectyper" name="ectyper" version="2.0">
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2 <requirements>
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3 <requirement type="package" version="3.6.3">python</requirement>
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4 <requirement type="package">ectyper</requirement>
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5 <requirement type="package">biopython</requirement>
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6 <requirement type="package">blast</requirement>
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7 <requirement type="package">samtools</requirement>
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8 <requirement type="package">bcftools</requirement>
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9 <requirement type="package">bowtie</requirement>
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10 <requirement type="package">spades</requirement>
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11 <requirement type="package">seqtk</requirement>
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12 <requirement type="package">pandas</requirement>
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13 <requirement type="package">mash</requirement>
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14 </requirements>
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15 <command detect_errors="exit_code"><![CDATA[
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16 #if $jobtype.select == "asm"
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17 ln -s $jobtype.draft sample.fasta;
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18 #else if $jobtype.select == "se"
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19 ln -s $jobtype.fastq1 sample_1.fastq;
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20 #else if $jobtype.select == "pe"
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21 ln -s $jobtype.fastq1 sample_1.fastq;
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22 ln -s $jobtype.fastq2 sample_2.fastq;
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23 #end if
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24
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25 python $__tool_directory__/bin/ectyper
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26 #if $jobtype.select == "asm"
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27 -m 4
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28 -i sample.fasta
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29 #else if $jobtype.select == "se"
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30 -m 3
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31 -i sample_1.fastq
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32 #else if $jobtype.select == "pe"
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33 -m 2
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34 -i sample_1.fastq sample_2.fastq
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35 #end if
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36 -b $maptype.select;
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37 cat ectyper_result*/ectyper_result.txt > results.txt;
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38
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39 ]]></command>
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40 <inputs>
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41 <conditional name="jobtype">
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42 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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43 <option value="asm">Genome Assembly</option>
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44 <option value="se">Single-End Reads</option>
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45 <option value="pe">Paired-End Reads</option>
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46 </param>
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47 <when value="asm">
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48 <param name="draft" type="data" format="fasta" label="FASTA" />
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49 </when>
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50 <when value="se">
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51 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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52 </when>
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53 <when value="pe">
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54 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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55 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
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56 </when>
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57 </conditional>
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58
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59 <conditional name="maptype">
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60 <param name="select" type="select" label="Algorithms for BWA mapping?">
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61 <option value="sam">sam</option>
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62 <option value="mem">mem</option>
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63 </param>
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64 </conditional>
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65
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66
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67 </inputs>
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68 <outputs>
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69 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <output name="results" file="results.txt"/>
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77
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78 **Usage: ectyper**
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79
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80 **INPUT**
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81
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82 A fasta assembly
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83
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84 **PERCENTIDENTITY**
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85
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86 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
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87
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88 **PERCENTLENGTH**
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89
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90 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
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91
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92 **verify**
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93
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94 Enable E. Coli. verification
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95
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96 **species**
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97
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98 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time.
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99
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100 **OUTPUT**
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101 Directory location of output files.
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102 ]]></help>
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103 </tool>
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