Mercurial > repos > cstrittmatter > skesa

annotate skesa.xml @ 1:abe89c222f28 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
author cstrittmatter
date Mon, 13 Aug 2018 17:28:32 -0400
parents 5bba9b6003cb
children 2f4443bea09d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
1 <tool id="skesa" name="skesa" version="0.1">
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
2 <requirements>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
3 <requirement type="package" version="0.1">skesa</requirement>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
4 </requirements>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
6 #if $jobtype.select != "cl"
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
7 skesa
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
8 #if $jobtype.select == "asm"
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
9 -i ${draft.name}.fasta
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
10 #else if $jobtype.select == "se"
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
11 --fastq ${fastq1.name}.fastq
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
12 #else if $jobtype.select == "pe"
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
13 --fastq ${fastq1.name}.fastq,${fastq2.name}.fastq
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
14 #end if
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
15 --use_paired_ends > results.skesa.fasta
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
16 #end if
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
17
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
18 ]]></command>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
19 <inputs>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
20 <conditional name="jobtype">
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
21 <param name="select" type="select" label="Assembly or FASTQ Reads?">
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
22 <option value="asm">Genome Assembly</option>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
23 <option value="se">Single-End Reads</option>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
24 <option value="pe">Paired-End Reads</option>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
25 <option value="cl">Collection of Reads</option>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
26 </param>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
27 <when value="asm">
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
28 <param name="draft" type="data" format="fasta" label="FASTA" />
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
29 </when>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
30 <when value="se">
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
31 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
32 </when>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
33 <when value="pe">
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
34 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
35 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
36 </when>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
37 <when value="cl">
1
abe89c222f28 planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents: 0
diff changeset
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" />
0
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
39 </when>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
40 </conditional>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
41
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
42 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
43 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
44
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
45 </inputs>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
46 <outputs>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
47 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
48 </outputs>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
49
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
50 <help><![CDATA[
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
51
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
52 **Usage: skesa**
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
53
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
54 **INPUT**
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
55
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
56 A fasta assembly or single or paired end reads test or data set list of fastqs
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
57
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
58 **PERCENTIDENTITY**
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
59
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
60 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
61
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
62 **PERCENTLENGTH**
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
63
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
64 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
65
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
66 https://github.com/phac-nml/ecoli_serotyping
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
67
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
68 ]]></help>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
69 <citations>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
70 <citation type="bibtex">
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
71 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
72 title={SRST2: ecyper wraps a standalone serotyping module for Escherichia coli. Supports fasta and fastq file formats.},
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
73 url={https://www.nml-lnm.gc.ca/},
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
74 author={National Microbiology Laboratory },
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
75 }</citation>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
76 </citations>
5bba9b6003cb planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
diff changeset
77 </tool>