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"planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 6615f6e5ae2eac1f8e90f25e1707c8b7ab161517"
author nml
date Fri, 29 May 2020 13:09:54 -0400
parents fb3683870b74
children
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08d801182fa1 "planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 6615f6e5ae2eac1f8e90f25e1707c8b7ab161517"
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1 <tool id="ectyper" name="ectyper" version="1.0.0">
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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="1.0.0">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 $adv_param.mash_input
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24 ln -s "${adv_param.mash_input}" mash_sketch.msh &&
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25 #end if
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28 #if $adv_param.db_input
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29 ln -s "${adv_param.db_input}" custom_db.json &&
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30 #end if
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32
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33 ectyper --cores \${GALAXY_SLOTS:-4}
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34 --input "${genomes}"
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35 -opid '$adv_param.opid'
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36 -opcov '$adv_param.opcov'
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37 -hpid '$adv_param.hpid'
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38 -hpcov '$adv_param.hpcov'
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39
0
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40 #if $adv_param.verifyEcoli
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41 --verify
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42 #end if
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43
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44 #if $adv_param.mash_input
1
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45 --refseq mash_sketch.msh
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46 #end if
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47
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48 #if $adv_param.db_input
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49 --dbpath custom_db.json
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50 #end if
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51
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52 --output '.'
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53 ]]>
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54 </command>
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55 <inputs>
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56 <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/>
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57 <section name="adv_param" title="Advanced parameters" expanded="False">
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58 <param name="opid" label="O antigen minimum %identity" type="integer" value="90" min="1" max="100"/>
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59 <param name="opcov" label="O antigen minimum %coverage" type="integer" value="90" min="1" max="100"/>
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60 <param name="hpid" label="H antigen minimum %identity" type="integer" value="95" min="1" max="100"/>
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61 <param name="hpcov" label="H antigen minimum %coverage" type="integer" value="50" min="1" max="100"/>
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62 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
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63 <param name="blastresults" type="boolean" checked="false" label="Include BLAST allele alignment results tab-delim file in the outputs?" />
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64 <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" />
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65 <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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66 <param name="db_input" type="data" optional="true" format="json" label="Custom database of alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/>
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67 </section>
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68 </inputs>
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69 <outputs>
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70 <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data>
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71 <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}">
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72 <filter>adv_param['logging']==True</filter>
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73 </data>
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74 <data name="output_blast" format="tabular" from_work_dir="blast_output_alleles.txt" label="${tool.name} BLAST results file on ${input.element_identifier}">
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75 <filter>adv_param['blastresults']==True</filter>
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76 </data>
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77 </outputs>
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78 <tests>
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79 <test>
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80 <param name="input" value="Escherichia2.fastq"/>
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81 <assert_stderr>
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82 <has_text text="O22"/>
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83 <has_text text="H8"/>
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84 </assert_stderr>
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85 <output name="output_result" ftype="tabular" >
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86 <assert_contents>
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87 <has_text_matching expression="O22"/>
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88 </assert_contents>
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89 </output>
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90 </test>
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91 </tests>
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92
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93 <help>
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94 **Syntax**
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95
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96
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97 This tool identifies the serotype of both assembled or assembly-free Escherichia coli genome samples based on a set of the key O and H antigen determinant genes including *wzm/wzt* or *wzx/wzy* and *fliC/flkA/flmA*.
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98 Unique to the tool, species identification module allows for non-E.coli genomes identification including other Escherichia genus species.
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99 This version improves antigen call rates on "difficult samples" by use of an adaptive threshold. This is especially useful when antigen genes are truncated or poorly covered by raw reads.
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100 If no antigen call is being predicted by the tool, try to lower %coverage parameter first. For more information on the new Quality Control module and running parameter details please visit https://github.com/phac-nml/ecoli_serotyping.
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101
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102
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103 -----
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104
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105 **Input:**
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106
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107 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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108
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109
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110 The default MASH RefSeq genome sketch (https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh) containing approximately 91K genomes is included and automatically updated every 6 months.
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111
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112
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113
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114 **Output:**
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115
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116 Tab-delimited report listing identified O and H antigens together with corresponding the highest-scoring alleles and normalized BLAST score defined as (%identity x %coverage) / 1e4.
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117 If *verifyEcoli* parameter is enabled, final report will contain allele quality control information on results for reporting purposes. PASS (REPORTABLE) QC flag means that O and H antigen calls are of sufficient to unambiguously resolve them from all other antigens.
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118
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119 -----
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120
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121 **Parameters (Optional):**
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122 - **Enable E. coli species verification:** for species verification in case samples are of non-E.coli origin
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123 - **Include BLAST allele alignment results tab-delim file in the outputs?** Get reference allele sequences and detailed BLAST output
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124 - **Include log file in the run outputs?:** Get optional logs of the ectyper run for a more detailed results assessment and troubleshooting
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125
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126 </help>
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127 <citations>
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128 <citation type="bibtex">
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129 @misc{githubectyper,
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130 author = {Laing Chad},
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131 title = {ECtyper - serotyping module for Escherichia coli},
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132 publisher = {GitHub},
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133 journal = {GitHub repository},
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134 url = {https://github.com/phac-nml/ecoli_serotyping}
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135 }</citation>
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136 </citations>
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137 </tool>