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annotate ectyper.xml @ 3:fb3683870b74 draft

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"planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5d7803f7bcc97c68dea824e08651ac536a6dbccb"
author nml
date Mon, 30 Dec 2019 10:10:44 -0500
parents e79a8dad83b4
children 08d801182fa1
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fb3683870b74 "planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5d7803f7bcc97c68dea824e08651ac536a6dbccb"
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1 <tool id="ectyper" name="ectyper" version="0.9.1">
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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>
3
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4 <requirement type="package" version="0.9.1">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}" "${i.element_identifier}" &&
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12 #if len($genomes) > 0
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13 #set $genomes = $genomes + ',' + str($i.element_identifier)
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14 #else
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15 #set $genomes = str($i.element_identifier)
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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.element_identifier}" &&
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20 #set $genomes = $input.element_identifier
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21 #end if
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22
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23 #if $mash_input
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24 ln -s "${mash_input}" mash_sketch.msh &&
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25 #end if
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26
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27 ectyper --cores \${GALAXY_SLOTS:-4}
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28 --input "${genomes}"
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29 --percentIdentity '$adv_param.min_percentIdentity'
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30 --percentLength '$adv_param.percentLength'
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31 #if $adv_param.verifyEcoli
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32 --verify
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33 #end if
1
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34 #if $mash_input
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35 --refseq mash_sketch.msh
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36 #end if
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37 #if $adv_param.alleleSequence
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38 --sequence
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39 #end if
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40 --output '.'
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41 ]]>
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42 </command>
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43 <inputs>
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44 <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/>
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45 <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/>
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46 <section name="adv_param" title="Advanced parameters" expanded="False">
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47 <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
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48 <param name="percentLength" type="integer" value="10" min="1" max="100"/>
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49 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
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50 <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/>
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51 <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" />
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52 </section>
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53 </inputs>
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54 <outputs>
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55 <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data>
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56 <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}">
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57 <filter>adv_param['logging']==True</filter>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input" value="Escherichia2.fastq"/>
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63 <assert_stderr>
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64 <has_text text="O22"/>
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65 <has_text text="H8"/>
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66 </assert_stderr>
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67 <output name="output_result" ftype="tabular" >
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68 <assert_contents>
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69 <has_text_matching expression="O22"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74
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75 <help>
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76 **Syntax**
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77
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79 This tool identifies the serotype of assembled or assembly-free Escherichia coli genome sample based on a set of either *wzm/wzt* or *wzx/wzy* and *fliC/flkA/flmA* alleles corresponding to O and H antigens, respectively.
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80 The non-E.coli genomes and other Escherichia genus species are successfully identified and well handled. The 0.9.0 version improves tool sensitivy when target alleles are truncated or
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81 poorly covered by raw reads.
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82
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83
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84 For more information please visit https://github.com/phac-nml/ecoli_serotyping.
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85
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86 -----
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87
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88 **Input:**
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89
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90 Accepts a variety of inputs including both single and/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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91
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92 The default MASH RefSeq genome sketch is included and updated every 6 months, but one can supply custom sketch file for species identification.
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94 One can download RefSeq genome sketch containing approximately 91,283 genomes from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh.
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95
0
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96
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97 **Output:**
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98
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99 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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100
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101 -----
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102
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103 **Parameters (Optional):**
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104
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105 - **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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106 - **Enable E. coli species verification:** Turn ON/OFF for more rigorous species verification (recommended)
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107 - **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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108
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109 </help>
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110 <citations>
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111 <citation type="bibtex">
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112 @misc{githubectyper,
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113 author = {Laing Chad},
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114 title = {ECtyper - serotyping module for Escherichia coli},
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115 publisher = {GitHub},
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116 journal = {GitHub repository},
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117 url = {https://github.com/phac-nml/ecoli_serotyping}
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118 }</citation>
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119 </citations>
2
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120 </tool>