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date Tue, 19 Sep 2017 16:34:57 -0400
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1 <tool id="stringmlst" name="StringMLST" version="1.1.0">
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2 <description>k-mer tool for multilocus sequence typing</description>
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3 <requirements>
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4 <requirement type="package" version="0.4.1">stringMLST</requirement>
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5 <requirement type="package" version="1.70">biopython</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11
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12
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13
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14 python $__tool_directory__/split_by_allele.py --alleles=$alleles --profiles=$scheme
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15 &&
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16 stringMLST.py --buildDB -c config.txt -k $kmer -P DB
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17
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18 &&
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19 #if $single_or_paired.type == "single"
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20 ln -s "$input_se" "$single_or_paired.input_se.element_identifier".fastq &&
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21
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22 stringMLST.py
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23 --predict
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24 -1 "$single_or_paired.input_se.element_identifier".fastq
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25 -s
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26 #elif $single_or_paired.type == "paired"
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27 ln -s "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln -s "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
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28 stringMLST.py
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29 --predict
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30 -1 "$single_or_paired.forward_pe.name"_1.fastq -2 "$single_or_paired.forward_pe.name"_2.fastq
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31 -p
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32 #else
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33 ln -s "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln -s "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
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34 stringMLST.py
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35 --predict
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36 -1 "$single_or_paired.fastq_collection.forward.name"_1.fastq -2 "$single_or_paired.fastq_collection.forward.name"_2.fastq
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37 -p
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38 #end if
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39 -o $output
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40 -r
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41 -P DB -k $kmer
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42
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43 ]]></command>
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44 <inputs>
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45 <conditional name="single_or_paired">
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46 <param name="type" type="select" label="Read type">
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47 <option value="single">Single-end</option>
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48 <option value="paired">Paired-end</option>
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49 <option value="collection">Collection Paired-end</option>
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50 </param>
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51 <when value="single">
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52 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
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53 </when>
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54 <when value="paired">
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55 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
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56 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
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57 </when>
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58 <when value="collection">
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59 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
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60 </when>
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61 </conditional>
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62 <param name="kmer" type="integer" label="K-mer to use" value="35" help=" Kmer length for which the db was created(Default k = 35)." />
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63 <param name="scheme" type="data" format="tabular" label="ST definitions for MLST scheme"/>
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64 <param name="alleles" type="data" format="fasta" label="Fasta file of MLST alleles"/>
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65
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66 </inputs>
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67 <outputs>
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68 <data format="tabular" name="output" label="Results"/>
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69 <data format="txt" name="log" label="Log" from_work_dir="DB.log"/>
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70 <data format="fastqsanger" name="reads" label='Reads' from_work_dir="*.fq" >
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71
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72 </data>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="scheme" value="st.tabular" />
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77 <param name="alleles" value="st.fasta" />
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78 <param name="input_se" value="input.fastqsanger" />
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79 <output file="results.tsv" ftype="tabular" name="output" />
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80 </test>
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81 </tests>
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82 <help><![CDATA[
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83 Original manual for command line available at http://jordan.biology.gatech.edu/page/software/stringmlst/stringMLST-useageDocumentation.pdf
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84 ]]>
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85
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86 </help>
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87 <citations>
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88 </citations>
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89 </tool>