Mercurial > repos > nml > ectyper

comparison ectyper.xml @ 0:b60c187a3a02 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
author nml
date Thu, 03 Jan 2019 15:21:29 -0500
parents
children b02c775b27c8
comparison
equal deleted inserted replaced
-1:000000000000 0:b60c187a3a02
1 <tool id="ectyper" name="ectyper" version="0.8.1">
2 <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
3 <requirements>
4 <requirement type="package" version="0.8.1">ectyper</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 #set $genomes = ''
9 #if hasattr($input, '__iter__')
10 #for $i in $input
11 ln -s "${i}" "${i.name}" &&
12 #if len($genomes) > 0
13 #set $genomes = $genomes + ',' + str($i.name)
14 #else
15 #set $genomes = str($i.name)
16 #end if
17 #end for
18 #else
19 ln -s "${input}" "${input.name}" &&
20 #set $genomes = $input.name
21 #end if
22
23 ectyper --cores \${GALAXY_SLOTS:-4}
24 --input "${genomes}"
25 --percentIdentity '$adv_param.min_percentIdentity'
26 --percentLength '$adv_param.percentLength'
27 #if $adv_param.verifyEcoli
28 --verify
29 #end if
30 #if $adv_param.alleleSequence
31 --sequence
32 #end if
33 --output '.'
34 ]]>
35 </command>
36 <inputs>
37 <param name="input" type="data" format="fastq,fasta" label="Input(s)" help="FASTA or FASTQ file(s) with contig(s)"/>
38 <section name="adv_param" title="Advanced parameters" expanded="False">
39 <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
40 <param name="percentLength" type="integer" value="50" min="1" max="100"/>
41 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
42 <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/>
43 <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" />
44 </section>
45 </inputs>
46 <outputs>
47 <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report"> </data>
48 <data name="output_log" format="text" from_work_dir="ectyper.log" label="${tool.name} log file">
49 <filter>adv_param['logging']==True</filter>
50 </data>
51 </outputs>
52 <tests>
53 <test>
54 <param name="input" value="Escherichia2.fastq"/>
55 <assert_stderr>
56 <has_text text="O22"/>
57 <has_text text="H8"/>
58 </assert_stderr>
59 <output name="output_result" ftype="tabular" >
60 <assert_contents>
61 <has_text_matching expression="O22"/>
62 </assert_contents>
63 </output>
64 </test>
65 </tests>
66
67 <help>
68 **Syntax**
69
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.
71
72 For more information please visit https://github.com/phac-nml/ecoli_serotyping.
73
74 -----
75
76 **Input:**
77
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.
79
80
81 **Output:**
82
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
84
85 -----
86
87 **Parameters (Optional):**
88
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
90 - **Enable E. coli species verification:** Turn ON/OFF for more rigorous species verification (recommended)
91 - **Include log file in the run outputs?:** Turn ON/OFF optional output of the ectyper log file for a more detailed results assessment
92
93 </help>
94 <citations>
95 <citation type="bibtex">
96 @misc{githubectyper,
97 author = {Laing Chad},
98 title = {ECtyper - serotyping module for Escherichia coli},
99 publisher = {GitHub},
100 journal = {GitHub repository},
101 url = {https://github.com/phac-nml/ecoli_serotyping}
102 }</citation>
103 </citations>
104 </tool>