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annotate stringmlst.xml @ 0:fc0f15ca12e0 draft

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author nml
date Mon, 24 Oct 2016 13:15:20 -0400
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1 <tool id="stringmlst" name="StringMLST" version="1.0.4">
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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="2.1">stringmlst</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10
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11
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12
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13 python $__tool_directory__/split_by_allele.py --alleles=$alleles --profiles=$scheme
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14 &&
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15 stringMLST.py --buildDB -c config.txt -k $kmer -P DB
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16
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17 &&
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18 #if $single_or_paired.type == "single"
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19 ln -s "$input_se" "$single_or_paired.input_se.element_identifier".fastq &&
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20
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21 stringMLST.py
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22 --predict
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23 -1 "$single_or_paired.input_se.element_identifier".fastq
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24 -s
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25 #elif $single_or_paired.type == "paired"
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26 ln -s "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln -s "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
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27 stringMLST.py
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28 --predict
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29 -1 "$single_or_paired.forward_pe.name"_1.fastq -2 "$single_or_paired.forward_pe.name"_2.fastq
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30 -p
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31 #else
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32 ln -s "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln -s "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
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33 stringMLST.py
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34 --predict
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35 -1 "$single_or_paired.fastq_collection.forward.name"_1.fastq -2 "$single_or_paired.fastq_collection.forward.name"_2.fastq
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36 -p
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37 #end if
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38 -o $output
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39 -r
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40 -P DB -k $kmer
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41
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42 ]]></command>
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43 <inputs>
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44 <conditional name="single_or_paired">
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45 <param name="type" type="select" label="Read type">
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46 <option value="single">Single-end</option>
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47 <option value="paired">Paired-end</option>
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48 <option value="collection">Collection Paired-end</option>
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49 </param>
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50 <when value="single">
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51 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
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52 </when>
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53 <when value="paired">
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54 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
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55 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
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56 </when>
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57 <when value="collection">
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58 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
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59 </when>
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60 </conditional>
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61 <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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62 <param name="scheme" type="data" format="tabular" label="ST definitions for MLST scheme"/>
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63 <param name="alleles" type="data" format="fasta" label="Fasta file of MLST alleles"/>
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64
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65 </inputs>
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66 <outputs>
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67 <data format="tabular" name="output" label="Results"/>
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68 <data format="txt" name="log" label="Log" from_work_dir="DB.log"/>
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69 <data format="fastqsanger" name="reads" label='Reads' from_work_dir="*.fq" >
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70
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="scheme" value="st.tabular" />
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76 <param name="alleles" value="st.fasta" />
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77 <param name="input_se" value="input.fastqsanger" />
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78 <output file="results.tsv" ftype="tabular" name="output" />
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 Original manual for command line available at http://jordan.biology.gatech.edu/page/software/stringmlst/stringMLST-useageDocumentation.pdf
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83 ]]>
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84
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85 </help>
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86 <citations>
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87 </citations>
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88 </tool>