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annotate skesa.xml @ 2:2f4443bea09d draft

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author cstrittmatter
date Mon, 13 Aug 2018 20:19:27 -0400
parents abe89c222f28
children c546fef7fd13
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1 <tool id="skesa" name="skesa" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="2.2">skesa</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 #if $jobtype.select != "cl"
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7 skesa
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8 #if $jobtype.select == "asm"
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9 -i ${draft.name}.fasta
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10 #else if $jobtype.select == "se"
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11 --fastq ${fastq1.name}.fastq
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12 #else if $jobtype.select == "pe"
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13 --fastq ${fastq1.name}.fastq,${fastq2.name}.fastq
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14 #end if
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15 --use_paired_ends > results.skesa.fasta
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16 #end if
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17
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18 ]]></command>
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19 <inputs>
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20 <conditional name="jobtype">
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21 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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22 <option value="asm">Genome Assembly</option>
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23 <option value="se">Single-End Reads</option>
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24 <option value="pe">Paired-End Reads</option>
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25 <option value="cl">Collection of Reads</option>
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26 </param>
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27 <when value="asm">
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28 <param name="draft" type="data" format="fasta" label="FASTA" />
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29 </when>
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30 <when value="se">
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31 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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32 </when>
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33 <when value="pe">
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34 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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35 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
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36 </when>
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37 <when value="cl">
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38 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
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39 </when>
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40 </conditional>
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41
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42 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
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43 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
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44
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45 </inputs>
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46 <outputs>
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47 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
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48 </outputs>
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49
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50 <help><![CDATA[
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51
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52 **Usage: skesa**
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53
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54 **INPUT**
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55
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56 A fasta assembly or single or paired end reads test or data set list of fastqs
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57
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58 **PERCENTIDENTITY**
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59
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60 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
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61
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62 **PERCENTLENGTH**
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63
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64 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
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65
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66 https://github.com/phac-nml/ecoli_serotyping
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67
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68 ]]></help>
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69 <citations>
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70 <citation type="bibtex">
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71 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
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72 title={SRST2: ecyper wraps a standalone serotyping module for Escherichia coli. Supports fasta and fastq file formats.},
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73 url={https://www.nml-lnm.gc.ca/},
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74 author={National Microbiology Laboratory },
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75 }</citation>
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76 </citations>
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77 </tool>