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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author rnateam
date Tue, 06 Dec 2016 11:39:14 -0500
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-1:000000000000 0:59055c49a112
1 <tool id="mlocarna" name="LocARNA" version="@VERSION@.0">
2 <description>
3 Multiple Alignment and Folding of RNAs
4 </description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <expand macro="stdio" />
13
14 <expand macro="version" />
15
16 <command><![CDATA[
17 mlocarna
18
19 '$input_data'
20 #if 'stockholm' in str($outputs).split(","):
21 --stockholm
22 #end if
23
24 --tgtdir 'outdir'
25
26 ## -------------------- alignment mode and specific options
27
28 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
29 $alignment_mode.free_endgaps
30 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
31 --sequ-local on
32 #else if str($alignment_mode.alignment_mode_selector) == "probabilistic"
33 --probabilistic
34 $alignment_mode.consistency_transformation
35
36 #if str($alignment_mode.iterate) == "true"
37 --iterate
38 --iterations $alignment_mode.iterations
39 #end if
40 #else if str($alignment_mode.alignment_mode_selector) == "sparse"
41 --sparse
42 #end if
43
44 ## -------------------- scoring parameters
45
46 --indel $Scoring.indel
47 --indel-opening $Scoring.indel_opening
48 --struct-weight $Scoring.struct_weight
49 --tau $Scoring.tau
50
51 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
52 --match $Scoring.sequence_score.match
53 --mismatch $Scoring.sequence_score.mismatch
54 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
55 --use-ribosum true
56 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
57 --ribofit true
58 #end if
59
60 ## -------------------- folding parameters
61
62 #if $Folding.plfold_span>=0
63 --plfold-span $Folding.plfold_span
64 --plfold-winsize $Folding.plfold_winsize
65 #end if
66
67 --rnafold-temperature $Folding.rnafold_temperature
68
69 ## -------------------- heuristic parameters
70
71 -p $Heuristics.min_prob
72 --max-diff-am $Heuristics.max_diff_am
73 --max-diff $Heuristics.max_diff
74 --max-diff-at-am $Heuristics.max_diff_at_am
75 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
76
77 $Heuristics.alifold_consensus_dp
78
79 ## -------------------- other parameters
80
81 $Other.lonely_pairs
82
83 $stdout_verbosity
84
85 #if str($stdout_verbosity) != "--quiet":
86 > '$stdout'
87 #end if
88 ]]></command>
89
90 <inputs>
91 <param name="input_data" type="data" format="text,fasta" label="Sequence input"
92 help="Sequence input in fasta format, optionally with locarna-specific extensions"
93 />
94
95 <conditional name="alignment_mode">
96 <param name="alignment_mode_selector" type="select" label="Alignment mode">
97 <option value="global_locarna">Global alignment (LocARNA)</option>
98 <option value="local_locarna">Local alignment (LocARNA)</option>
99 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
100 <option value="sparse">Global alignment (SPARSE)</option>
101 </param>
102 <when value="global_locarna">
103 <param name="free_endgaps" type="select" label="Free endgaps">
104 <option value="">No free endgaps</option>
105 <option value="--free-endgaps">Free endgaps</option>
106 <option value="--free-endgaps-5">Free endgaps, only 5'</option>
107 <option value="--free-endgaps-3">Free endgaps, only 3'</option>
108 </param>
109 </when>
110 <when value="local_locarna" />
111 <when value="probabilistic">
112 <param name="consistency_transformation" type="boolean"
113 truevalue="--consistency-transformation" falsevalue=""
114 checked="true" label="Consistency transformation"
115 help="--consistency-transformation" />
116 <param name="iterate" type="boolean"
117 truevalue="true" falsevalue="false"
118 checked="false" label="Iterative refinement"
119 help="--iterate" />
120 <param name="iterations" type="integer"
121 value="1" label="Number of refinement iterations"
122 help="--iterations num" />
123 </when>
124 <when value="sparse" />
125 </conditional>
126
127 <param name="outputs" type="select" display="checkboxes" multiple="True"
128 label="Output options">
129 <option value="clustal" selected="True">Output alignment
130 in Clustalw format</option>
131 <option value="stockholm" selected="False">Output
132 alignment in Stockholm format</option>
133 </param>
134
135 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
136 <option value="--quiet">Don't report standard
137 output</option>
138 <option value="">Non verbose</option>
139 <option value="--verbose">Verbose</option>
140 <option value="--moreverbose">More verbose</option>
141 </param>
142
143
144 <section name="Scoring" title="Scoring parameters">
145 <expand macro="common_scoring_parameters" />
146 </section>
147
148 <section name="Folding" title="RNA folding parameters">
149 <expand macro="common_folding_parameters" />
150 </section>
151
152 <section name="Heuristics" title="Heuristic parameters">
153 <expand macro="common_heuristic_parameters" />
154 </section>
155
156 <section name="Other" title="Other parameters">
157 <expand macro="common_other_parameters" />
158 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP"
159 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
160 </section>
161 </inputs>
162
163 <outputs>
164 <expand macro="common_outputs" />
165 </outputs>
166
167 <tests>
168 <test>
169 <param name="input_data" value="archaea.fa" />
170 <param name="stdout_verbosity" value="" />
171 <output name="stdout" file="archaea-default.stdout" />
172 </test>
173 <test>
174 <param name="input_data" value="haca.snoRNA.fa" />
175 <param name="stdout_verbosity" value="" />
176 <output name="stdout" file="haca.snoRNA-default.stdout" />
177 </test>
178 <test>
179 <param name="input_data" value="archaea.fa" />
180 <param name="stdout_verbosity" value="" />
181 <param name="outputs" value="clustal" />
182 <param name="alignment_mode_selector" value="probabilistic" />
183 <output name="clustal" file="archaea-probabilistic.aln" />
184 </test>
185 </tests>
186
187 <help><![CDATA[ **Multiple alignment of RNAs**
188
189 For more information, see
190 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
191 ]]></help>
192
193 <expand macro="citations" />
194
195 </tool>