Mercurial > repos > nml > ectyper

annotate ectyper.xml @ 0:b60c187a3a02 draft

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planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
author nml
date Thu, 03 Jan 2019 15:21:29 -0500
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0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
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1 <tool id="ectyper" name="ectyper" version="0.8.1">
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2 <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
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3 <requirements>
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4 <requirement type="package" version="0.8.1">ectyper</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 #set $genomes = ''
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9 #if hasattr($input, '__iter__')
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10 #for $i in $input
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11 ln -s "${i}" "${i.name}" &&
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12 #if len($genomes) > 0
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13 #set $genomes = $genomes + ',' + str($i.name)
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14 #else
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15 #set $genomes = str($i.name)
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16 #end if
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17 #end for
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18 #else
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19 ln -s "${input}" "${input.name}" &&
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
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20 #set $genomes = $input.name
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21 #end if
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22
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23 ectyper --cores \${GALAXY_SLOTS:-4}
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24 --input "${genomes}"
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25 --percentIdentity '$adv_param.min_percentIdentity'
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26 --percentLength '$adv_param.percentLength'
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27 #if $adv_param.verifyEcoli
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28 --verify
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29 #end if
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30 #if $adv_param.alleleSequence
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31 --sequence
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32 #end if
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33 --output '.'
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param name="input" type="data" format="fastq,fasta" label="Input(s)" help="FASTA or FASTQ file(s) with contig(s)"/>
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38 <section name="adv_param" title="Advanced parameters" expanded="False">
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39 <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
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40 <param name="percentLength" type="integer" value="50" min="1" max="100"/>
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41 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
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42 <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/>
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43 <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" />
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44 </section>
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45 </inputs>
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46 <outputs>
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47 <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report"> </data>
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48 <data name="output_log" format="text" from_work_dir="ectyper.log" label="${tool.name} log file">
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49 <filter>adv_param['logging']==True</filter>
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50 </data>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="input" value="Escherichia2.fastq"/>
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55 <assert_stderr>
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56 <has_text text="O22"/>
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57 <has_text text="H8"/>
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58 </assert_stderr>
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59 <output name="output_result" ftype="tabular" >
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60 <assert_contents>
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61 <has_text_matching expression="O22"/>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66
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67 <help>
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68 **Syntax**
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69
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70 This tool identifies the serotype of Escherichia coli genome sequences based on a set of *wzm/wzt*, *wzx/wzy* and *fliC/flkA/flmA* alleles corresponding to O and H antigens, respectively.
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71
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72 For more information please visit https://github.com/phac-nml/ecoli_serotyping.
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73
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74 -----
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75
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76 **Input:**
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77
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78 Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended.
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79
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80
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81 **Output:**
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82
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83 Tab-delimited report listing identified O and H antigens together with corresponding highest scoring alleles and normalized BLAST score defined as (%identity x query coverage length) / 10000
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84
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85 -----
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86
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87 **Parameters (Optional):**
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88
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89 - **Print the allele sequences as the final columns of the output?** Turn ON/OFF addition of the actual O and H antigen allelic sequences in the report
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90 - **Enable E. coli species verification:** Turn ON/OFF for more rigorous species verification (recommended)
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91 - **Include log file in the run outputs?:** Turn ON/OFF optional output of the ectyper log file for a more detailed results assessment
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92
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93 </help>
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94 <citations>
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95 <citation type="bibtex">
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96 @misc{githubectyper,
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97 author = {Laing Chad},
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98 title = {ECtyper - serotyping module for Escherichia coli},
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99 publisher = {GitHub},
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100 journal = {GitHub repository},
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101 url = {https://github.com/phac-nml/ecoli_serotyping}
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102 }</citation>
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103 </citations>
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104 </tool>