Mercurial > repos > nml > ectyper

annotate ectyper.xml @ 1:b02c775b27c8 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 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
author nml
date Thu, 31 Jan 2019 09:39:04 -0500
parents b60c187a3a02
children e79a8dad83b4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
1 <tool id="ectyper" name="ectyper" version="0.8.1">
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
2 <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
3 <requirements>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
4 <requirement type="package" version="0.8.1">ectyper</requirement>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
5 </requirements>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
6 <command detect_errors="exit_code">
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
7 <![CDATA[
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
8 #set $genomes = ''
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
9 #if hasattr($input, '__iter__')
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
10 #for $i in $input
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
11 ln -s "${i}" "${i.name}" &&
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
12 #if len($genomes) > 0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
13 #set $genomes = $genomes + ',' + str($i.name)
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
14 #else
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
15 #set $genomes = str($i.name)
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
16 #end if
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
17 #end for
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
18 #else
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
19 ln -s "${input}" "${input.name}" &&
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
20 #set $genomes = $input.name
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
21 #end if
1
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
22
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
23 #if $mash_input
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
24 ln -s "${mash_input}" mash_sketch.msh &&
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
25 #end if
0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
26
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
27 ectyper --cores \${GALAXY_SLOTS:-4}
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
28 --input "${genomes}"
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
29 --percentIdentity '$adv_param.min_percentIdentity'
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
30 --percentLength '$adv_param.percentLength'
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
31 #if $adv_param.verifyEcoli
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
32 --verify
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
33 #end if
1
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
34 #if $mash_input
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
35 --refseq mash_sketch.msh
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
36 #end if
0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
37 #if $adv_param.alleleSequence
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
38 --sequence
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
39 #end if
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
40 --output '.'
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
41 ]]>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
42 </command>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
43 <inputs>
1
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
44 <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s) with contig(s)"/>
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
45 <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide MASH sketches to find closest genome (in case O/H typing fails)"/>
0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
46 <section name="adv_param" title="Advanced parameters" expanded="False">
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
47 <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
48 <param name="percentLength" type="integer" value="50" min="1" max="100"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
49 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
50 <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
51 <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" />
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
52 </section>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
53 </inputs>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
54 <outputs>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
55 <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report"> </data>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
56 <data name="output_log" format="text" from_work_dir="ectyper.log" label="${tool.name} log file">
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
57 <filter>adv_param['logging']==True</filter>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
58 </data>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
59 </outputs>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
60 <tests>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
61 <test>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
62 <param name="input" value="Escherichia2.fastq"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
63 <assert_stderr>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
64 <has_text text="O22"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
65 <has_text text="H8"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
66 </assert_stderr>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
67 <output name="output_result" ftype="tabular" >
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
68 <assert_contents>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
69 <has_text_matching expression="O22"/>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
70 </assert_contents>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
71 </output>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
72 </test>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
73 </tests>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
74
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
75 <help>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
76 **Syntax**
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
77
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
78 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.
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
79
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
80 For more information please visit https://github.com/phac-nml/ecoli_serotyping.
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
81
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
82 -----
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
83
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
84 **Input:**
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
85
1
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
86 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.
0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
87
1
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
88 Optionally select a MASH RefSeq genome sketch (version 2.0 and above) for cases when O/H typing would fail. Download RefSeq genome sketch containing 91,283 genomes with 1000 hashes each directly from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh .
0
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
89
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
90 **Output:**
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
91
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
92 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
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
93
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
94 -----
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
95
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
96 **Parameters (Optional):**
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
97
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
98 - **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
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
99 - **Enable E. coli species verification:** Turn ON/OFF for more rigorous species verification (recommended)
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
100 - **Include log file in the run outputs?:** Turn ON/OFF optional output of the ectyper log file for a more detailed results assessment
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
101
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
102 </help>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
103 <citations>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
104 <citation type="bibtex">
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
105 @misc{githubectyper,
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
106 author = {Laing Chad},
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
107 title = {ECtyper - serotyping module for Escherichia coli},
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
108 publisher = {GitHub},
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
109 journal = {GitHub repository},
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
110 url = {https://github.com/phac-nml/ecoli_serotyping}
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
111 }</citation>
b60c187a3a02 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 5ea0a5bb5a06d5d4bec03de885cc47df72193f87
nml
parents:
diff changeset
112 </citations>
1
b02c775b27c8 planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
nml
parents: 0
diff changeset
113 </tool>