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planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
author yating-l
date Wed, 12 Apr 2017 17:37:47 -0400
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1 <tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="1.0">
2 <requirements>
3 <requirement type="package" version="1.0">snap</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8 <command><![CDATA[
9 snap
10 #if $settings.advanced == "advanced"
11 $settings.lcmask
12 #if $settings.strand == "true"
13 $settings.strand.onestrand
14 #end if
15 #end if
16 #if $proteins == "-aa":
17 $proteins "$output2"
18 #end if
19 #if $transcripts == "-tx":
20 $transcripts "$output3"
21 #end if
22 -gff
23 -quiet
24 $organism
25 $input1
26 | python $__tool_directory__/gff2Togff3.py --output $output1
27 ]]></command>
28 <inputs>
29 <param type="data" name="input1" format="fasta" />
30 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
31 <option value="A.gambiae.hmm">A.gambiae</option>
32 <option value="A.mellifera.hmm">A.mellifera</option>
33 <option value="A.thaliana.hmm">Arabidopsis thaliana</option>
34 <option value="Acanium.hmm">Acanium</option>
35 <option value="At.hmm">Thale</option>
36 <option value="B.malayi.hmm">Brugia</option>
37 <option value="B.mori.hmm">B.mori</option>
38 <option value="C.elegans.hmm">C.elegans</option>
39 <option value="C.intestinalis.hmm">Ciona</option>
40 <option value="Ce.hmm">Ce</option>
41 <option value="D.melanogaster.hmm">Drosophila melanogaster</option>
42 <option value="Dm.hmm">Dm</option>
43 <option value="ixodesA.hmm">ixodesA</option>
44 <option value="ixodesB.hmm">ixodesB</option>
45 <option value="mam39-ro.hmm">mam39-ro</option>
46 <option value="mam39.hmm">mam39</option>
47 <option value="mam46-ro.hmm">mam46-ro</option>
48 <option value="mam46.hmm">mam46</option>
49 <option value="mam54-ro.hmm">mam54-ro</option>
50 <option value="mam54.hmm">mam54</option>
51 <option value="mamiso.hmm">mamiso</option>
52 <option value="minimal.hmm">minimal</option>
53 <option value="Nasonia.hmm">Nasonia</option>
54 <option value="nGASP.hmm">nGASP</option>
55 <option value="nGASPr.hmm">nGASPr</option>
56 <option value="O.sativa.hmm">O.sativa</option>
57 <option value="Os.hmm">Os</option>
58 </param>
59 <param name="proteins" type="select" label="Create FASTA file of proteins">
60 <option value="">No</option>
61 <option value="-aa">Yes</option>
62 </param>
63 <param name="transcripts" type="select" label="Create FASTA file of transcripts">
64 <option value="">No</option>
65 <option value="-tx">Yes</option>
66 </param>
67 <conditional name="settings">
68 <param name="advanced" type="select" label="Specify advanced parameters">
69 <option value="simple" selected="true">No, use program defaults.</option>
70 <option value="advanced">Yes, see full parameter list.</option>
71 </param>
72 <when value="simple">
73 </when>
74 <when value="advanced">
75 <param name="lcmask" type="boolean" label="treat lowercase as N" truevalue="-lcmask" falsevalue="" />
76 <conditional name="strand">
77 <param name="strand" type="boolean" label="predict on one strand only" />
78 <when value="true">
79 <param name="onestrand" type="select" label="Specify which strand to predict">
80 <option value="-plus">predict on plus strand only.</option>
81 <option value="-minus">predict on minus strand only.</option>
82 </param>
83 </when>
84 <when value="false">
85 </when>
86 </conditional>
87 </when>
88 </conditional>
89 </inputs>
90 <outputs>
91 <data name="output1" format="gff3" label="${tool.name} on ${on_string}: GTF/GFF3">
92 </data>
93 <data name="output2" format="fasta" label="${tool.name} on ${on_string}: Protein sequence">
94 <filter>proteins == "-aa"</filter>
95 </data>
96 <data name="output3" format="fasta" label="${tool.name} on ${on_string}: Coding sequence">
97 <filter>transcripts == "-tx"</filter>
98 </data>
99 </outputs>
100 <tests>
101 <test>
102 <param name="input1" value="thale.dna.gz"/>
103 <param name="organism" value="At.hmm" />
104 <output name="output1" file="thale.gff3"/>
105 </test>
106 </tests>
107 <help><![CDATA[
108 The general form of the snap command line is:
109
110 snap <HMM file> <FASTA file> [options]
111
112 HMM file:
113
114 The most convenient way to specify the HMM file is by name. This requires
115 that the ZOE environment variable is set. In this case, snap will look
116 for the HMM file in $ZOE/HMM. You may also specify the HMM file by an
117 explicit path. The following are equivalent if $ZOE is in /usr/local:
118
119 snap C.elegans.hmm ...
120 snap /usr/local/Zoe/HMM/C.elegans.hmm ...
121 snap worm ... # there are a few convenient aliases in $ZOE/HMM
122
123 FASTA file:
124
125 If you have several sequences to analyze, it is more efficient to run
126 snap on a concatenated FASTA file rather than separate runs on single
127 sequence files. The seqeuence may be in a compressed format
128
129 If sequences have been masked with lowercase letters, use -lcmask to
130 prevent exons from appearing in masked DNA.
131
132 Output:
133
134 Annotation is reported to stdout in a non-standard format (ZFF). You can
135 change to GFF or ACEDB with the -gff or -ace options. Proteins and
136 transcripts are reported to FASTA files with the -aa and -tx options.
137
138 External definitions:
139
140 SNAP allows you to adjust the score of any sequence model at any point
141 in a sequence. This behavior is invoked by giving a ZFF file to SNAP:
142
143 snap <hmm> <sequence> -xdef <ZFF file>
144
145 Each feature description uses the 'group' field to issue a command:
146
147 SET set the score
148 ADJ adjust the score up or down
149 OK set non-cannonical scores
150
151 >FOO
152 Acceptor 120 120 + +50 . . . SET (sets an Acceptor to 50)
153 Donor 212 212 + -20 . . . ADJ (lowers a Donor by -20)
154 Inter 338 579 + -2 . . . ADJ (lowers Inter by -2 in a range)
155 Coding 440 512 - +3 . . . ADJ (raises Coding by +3 in a range)
156 Donor 625 638 + -5 . . . OK (sets range of odd Donors to -5)
157
158 If the output has scrolled off your screen, try 'snap -help | more'
159
160 ]]></help>
161 <citations>
162 <citation type="bibtex">
163 @misc{renameTODO,
164 author = {LastTODO, FirstTODO},
165 year = {TODO},
166 title = {TODO},
167 url = {http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz},
168 }</citation>
169 </citations>
170 </tool>