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planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
author cstrittmatter
date Mon, 13 Aug 2018 17:17:00 -0400
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1 <tool id="skesa" name="skesa" version="0.1">
2 <requirements>
3 <requirement type="package" version="0.1">skesa</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 #if $jobtype.select != "cl"
7 skesa
8 #if $jobtype.select == "asm"
9 -i ${draft.name}.fasta
10 #else if $jobtype.select == "se"
11 --fastq ${fastq1.name}.fastq
12 #else if $jobtype.select == "pe"
13 --fastq ${fastq1.name}.fastq,${fastq2.name}.fastq
14 #end if
15 --use_paired_ends > results.skesa.fasta
16 #end if
17
18 ]]></command>
19 <inputs>
20 <conditional name="jobtype">
21 <param name="select" type="select" label="Assembly or FASTQ Reads?">
22 <option value="asm">Genome Assembly</option>
23 <option value="se">Single-End Reads</option>
24 <option value="pe">Paired-End Reads</option>
25 <option value="cl">Collection of Reads</option>
26 </param>
27 <when value="asm">
28 <param name="draft" type="data" format="fasta" label="FASTA" />
29 </when>
30 <when value="se">
31 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
32 </when>
33 <when value="pe">
34 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
35 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
36 </when>
37 <when value="cl">
38 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
39 </when>
40 </conditional>
41
42 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
43 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
44
45 </inputs>
46 <outputs>
47 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
48 </outputs>
49
50 <help><![CDATA[
51
52 **Usage: skesa**
53
54 **INPUT**
55
56 A fasta assembly or single or paired end reads test or data set list of fastqs
57
58 **PERCENTIDENTITY**
59
60 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
61
62 **PERCENTLENGTH**
63
64 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
65
66 https://github.com/phac-nml/ecoli_serotyping
67
68 ]]></help>
69 <citations>
70 <citation type="bibtex">
71 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
72 title={SRST2: ecyper wraps a standalone serotyping module for Escherichia coli. Supports fasta and fastq file formats.},
73 url={https://www.nml-lnm.gc.ca/},
74 author={National Microbiology Laboratory },
75 }</citation>
76 </citations>
77 </tool>