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planemo upload commit 4fee4519135f7677cf50f721cf1ad7a7335ad66d-dirty
author nml
date Fri, 06 Apr 2018 14:29:17 -0400
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1 <tool id="pseudogenome" name="Create pseudo genome" version="1.0.0">
2 <description>from a fasta file in order of appearance</description>
3 <requirements>
4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
5 <requirement type="package" version="1.04">perl-readonly</requirement>
6 <requirement type="package" version="2.49">perl-getopt-long</requirement>
7 <requirement type="package" version="1.25">perl-ipc-system-simple</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 perl '$__tool_directory__/pseudogenome.pl' -i '$input'
11
12 #if $stitch.howto == "jcvi":
13 -s
14 #else
15 -n '$stitch.number' -c '$stitch.glue'
16 #end if
17
18 -o '$output'
19 ]]></command>
20 <inputs>
21 <param name="input" type="data" format="fasta" label="Multi contig fasta file" optional="false"/>
22
23 <conditional name="stitch">
24 <param name="howto" type="select" label="How do you want to merge contigs?">
25 <option selected="true" value="jcvi">JCVI Linker</option>
26 <option value="custom">Custom options</option>
27 </param>
28 <when value="jcvi">
29 </when>
30 <when value="custom">
31 <param name="number" type="integer" value="10" label="Number of filler base pairs" optional="false"/>
32 <param name="glue" type="text" value="N" label="Character inserted between contigs" optional="false"/>
33 </when>
34 </conditional>
35 </inputs>
36 <outputs>
37 <data format="fasta" name="output"/>
38 </outputs>
39 <tests>
40 <test>
41 <param name="input" value="input.fasta"/>
42 <output name="output" value="output.fasta"/>
43 </test>
44 <test>
45 <param name="input" value="input.fasta"/>
46 <param name="howto" value="custom"/>
47 <param name="number" value="50"/>
48 <param name="glue" value="X"/>
49 <output name="output" value="custom.fasta"/>
50 </test>
51 </tests>
52 <help>
53
54 What it does
55 ============
56 This tool takes in a mult-contig fasta file and converts it into a pseudo genome.
57
58
59
60 JCVI Linker
61 ============
62
63 Linker is a 36 base pair sequence which places start and
64 stop codons in all 6 reading frames to prevent gene for being predicted across contigs.
65
66 Sequence below:
67
68 "NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN"
69
70 </help>
71 <citations>
72 </citations>
73 </tool>