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comparison macros.xml @ 0:e91e4f48875e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author rnateam
date Fri, 13 Jan 2017 16:49:16 -0500
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children 8723e3f8e422
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-1:000000000000 0:e91e4f48875e
1 <macros>
2 <token name="@VERSION@">1.9.0</token>
3
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@VERSION@">locarna</requirement>
7 </requirements>
8 </xml>
9
10 <xml name="stdio">
11 <stdio>
12 <exit_code range="1:" />
13 </stdio>
14 </xml>
15
16 <xml name="version">
17 <version_command>
18 <![CDATA[
19 mlocarna --version
20 ]]>
21 </version_command>
22 </xml>
23
24 <xml name="bed_anchors">
25 <conditional name="bed_anchors">
26 <param name="bed_anchors_selector" type="select" label="Anchor constraints"
27 help="Anchor constraints in bed format specify positions of
28 named anchor regions per sequence. The sequence names
29 ('contig' names have to correspond to the fasta input
30 sequence names. Anchor names must be unique per sequence
31 and regions of the same name for different sequences
32 must have the same length. This constrains the alignment
33 to align all regions of the same name.">
34 <option value="no">Don't load anchor constraints from
35 bed file</option>
36 <option value="yes">Load anchor constraints from bed
37 file</option>
38 </param>
39 <when value="no" />
40 <when value="yes">
41 <param name="bed_anchors_file" type="data" format="tabular"
42 label="Anchor constraint specification in bed format"
43 />
44 </when>
45 </conditional>
46 </xml>
47
48 <xml name="common_scoring_parameters">
49 <param name="struct_weight" argument="struct-weight"
50 label="Structure weight" type="integer"
51 value="200" min="0" max="800" />
52 <param name="indel_opening" argument="indel-opening"
53 label="Indel opening score" type="integer"
54 value="-500" max="0" min="-1500" />
55 <param argument="indel" label="Indel score" type="integer"
56 value="-350" min="-1000" max="0" />
57 <param argument="tau" type="integer" value="50"
58 min="0" max="200"
59 label="Sequence contribution at structure match in percent"/>
60
61 <conditional name="sequence_score">
62 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
63 <option value="ribofit">Use ribofit</option>
64 <option value="ribosum">Use RIBOSUM85_60</option>
65 <option value="match">Simple match/mismatch costs</option>
66 </param>
67 <when value="ribofit" />
68 <when value="ribosum" />
69 <when value="match">
70 <param name="match" type="integer" value="50"
71 min="0" max="400"
72 label="Match score" />
73 <param name="mismatch" type="integer" value="0"
74 min="-400" max="0"
75 label="Mismatch score" />
76 </when>
77 </conditional>
78 </xml>
79
80 <xml name="plfolding_parameters">
81 <param name="plfold_span" argument="--plfold-span"
82 type="integer" value="150" min="-1" max="400"
83 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
84
85 <param name="plfold_winsize" argument="--plfold-winsize"
86 type="integer" value="300" min="-1" max="800"
87 label="Window size for local folding" />
88 </xml>
89
90 <xml name="common_folding_parameters">
91 <param name="rnafold_temperature" argument="rnafold-temperature"
92 type="float" value="37.0" min="10" max="50"
93 label="Temperature for RNAfold (RNAfold's -T option)" />
94 </xml>
95
96 <token name="@SCORING_ARGS@">
97 ## -------------------- scoring parameters
98 --indel $Scoring.indel
99 --indel-opening $Scoring.indel_opening
100 --struct-weight $Scoring.struct_weight
101 --tau $Scoring.tau
102
103 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
104 --match $Scoring.sequence_score.match
105 --mismatch $Scoring.sequence_score.mismatch
106 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
107 --use-ribosum true
108 #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
109 --ribofit true
110 #end if
111 </token>
112
113 <token name="@FOLDING_ARGS@">
114 ## -------------------- folding parameters
115 #if float($Folding.rnafold_temperature) != 37.0
116 --rnafold-temperature $Folding.rnafold_temperature
117 #end if
118 </token>
119
120 <token name="@HEURISTIC_ARGS@">
121 ## -------------------- heuristic parameters
122 -p $Heuristics.min_prob
123
124 #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off"
125 --max-diff -1
126 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff"
127 --max-diff $Heuristics.max_diff_mode.max_diff
128 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am"
129 --max-diff -1
130 --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am
131 #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln"
132 --max-diff $Heuristics.max_diff_mode.max_diff
133 --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln'
134 $Heuristics.max_diff_mode.max_diff_relax
135 #end if
136
137 --max-diff-am $Heuristics.max_diff_am
138
139 #if float($Heuristics.max_bps_length_ratio) > 0.0
140 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
141 #end if
142 </token>
143
144 <token name="@CONSTRAINT_ARGS@">
145 ## -------------------- constraint parameters
146 $Constraints.lonely_pairs
147
148 #if $Constraints.maxBPspan != -1
149 --maxBPspan $Constraints.maxBPspan
150 #end if
151
152 $Constraints.ignore_constraints
153 </token>
154
155 <token name="@STDOUT_ARGS@">
156 $stdout_verbosity
157
158 #if str($stdout_verbosity) != "--quiet":
159 > '$stdout'
160 #end if
161 </token>
162
163 <xml name="max_diff_parameters_selector">
164 <param name="max_diff_mode_selector" type="select"
165 label="Restrict alignable positions by maximum difference"
166 help="(max-diff*)">
167 <option value="off">Off</option>
168 <option value="max-diff" selected="True">Maximal difference of aligned positions</option>
169 <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option>
170 <yield />
171 </param>
172 </xml>
173
174 <xml name="max_diff_parameters_standard_cases">
175 <when value="off" />
176 <when value="max-diff">
177 <param name="max_diff" argument="max-diff" type="integer"
178 value="60" min="-1" max="300"
179 label="Maximal difference of aligned positions" />
180 </when>
181 <when value="max-diff-at-am">
182 <param name="max_diff_at_am" argument="max-diff-at-am" type="integer"
183 value="60" min="-1" max="300"
184 label="Maximal difference of aligned positions,
185 only at arc match positions" />
186 </when>
187 </xml>
188
189 <xml name="max_diff_parameters">
190 <conditional name="max_diff_mode">
191 <expand macro="max_diff_parameters_selector" />
192 <expand macro="max_diff_parameters_standard_cases" />
193 </conditional>
194 </xml>
195
196 <xml name="max_diff_parameters_aln">
197 <conditional name="max_diff_mode">
198 <expand macro="max_diff_parameters_selector">
199 <option value="max-diff-aln">Maximal difference to a reference alignment</option>
200 </expand>
201 <expand macro="max_diff_parameters_standard_cases" />
202 <when value="max-diff-aln">
203 <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal"
204 label="Reference alignment"
205 />
206 <param name="max_diff" argument="max-diff" type="integer"
207 value="60" min="-1" max="300"
208 label="Maximal difference of aligned positions" />
209 <param name="max_diff_relax" argument="max-diff-relax" type="boolean"
210 truevalue="--max-diff-relax" falsevalue=""
211 checked="False"
212 label="Relax deviation constraints in multiple
213 aligmnent."
214 />
215 </when>
216 </conditional>
217 </xml>
218
219 <xml name="common_heuristic_parameters">
220 <param name="min_prob" argument="min-prob" type="float" value="0.0005"
221 min="0.0" max="0.2"
222 label="Minimal / cutoff probability" />
223
224 <param name="max_diff_am" argument="max-diff-am"
225 type="integer" value="30"
226 min="-1" max="300"
227 label="Maximal difference for sizes of matched arcs (-1=off)" />
228
229 <param name="max_bps_length_ratio" argument="max-bps-length-ratio"
230 type="float" value="0.0" min="0.0" max="10.0"
231 label="Maximal ratio 'number of considered base pairs' by
232 'sequence length' (default: 0.0 = no effect)" />
233 </xml>
234
235 <xml name="in_loop_ratio_parameters">
236 <param name="max_uil_length_ratio" argument="max-uil-length-ratio"
237 type="float" value="0.0" min="0.0" max="10.0"
238 label="Maximal ratio 'number considered unpaired bases in loops' by
239 'sequence length' (default: 0.0; no effect)" />
240
241 <param name="max_bpil_length_ratio" argument="max-bpil-length-ratio"
242 type="float" value="0.0" min="0.0" max="10.0"
243 label="Maximal ratio 'number of considered base pairs in loops'
244 by 'sequence length' (default: 0.0; no effect)" />
245 </xml>
246
247 <xml name="exparnap_in_loop_parameters">
248 <param name="prob_unpaired_in_loop_threshold"
249 argument="prob_unpaired_in_loop_threshold"
250 type="float" value="0.01" min="0.0" max="1.0"
251 label="Probability threshold for unpaired bases in loops" />
252 <param name="prob_basepair_in_loop_threshold"
253 argument="prob_basepair_in_loop_threshold"
254 type="float" value="0.01" min="0.0" max="1.0"
255 label="Probability threshold for base pairs in loops" />
256 </xml>
257
258 <xml name="alifold_consensus_parameter">
259 <param name="alifold_consensus_dp" argument="alifold-consensus-dp"
260 type="boolean" checked="False"
261 truevalue="--alifold-consensus-dp" falsevalue=""
262 label="Compute consensus dot plot by alifold" />
263 </xml>
264
265 <xml name="common_constraint_parameters">
266 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP"
267 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
268 <param name="maxBPspan" argument="--maxBPspan"
269 type="integer" value="-1" min="-1" max="400"
270 label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
271 <param name="ignore_constraints" argument="ignore-constraints"
272 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
273 help="Ignore all anchor and structure constraints given
274 in the fasta(-ish) input." />
275 </xml>
276
277 <xml name="standard_outupt">
278 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
279 <filter>stdout_verbosity != '--quiet'</filter>
280 </data>
281 </xml>
282
283 <xml name="mlocarna_outputs">
284 <expand macro="standard_outupt" />
285 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
286 label="${tool.name} alignment (annotated clustal) on ${on_string}">
287 <filter>'clustal' in outputs</filter>
288 </data>
289 <data format="clustal" name="clustal_strict"
290 from_work_dir="mlocarna_results/results/result.strict-aln"
291 label="${tool.name} alignment (clustal) on ${on_string}">
292 <filter>'clustal_strict' in outputs</filter>
293 </data>
294 <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
295 label="${tool.name} alignment (stockholm) on ${on_string}">
296 <filter>'stockholm' in outputs</filter>
297 </data>
298 <data format="txt" name="pp"
299 from_work_dir="mlocarna_results/results/result.pp"
300 label="${tool.name} alignment (PP 2.0) on ${on_string}">
301 <filter>'pp' in outputs</filter>
302 </data>
303 <data format="tar.gz" name="mlocarna_results_tgz"
304 label="${tool.name} results archive on ${on_string}">
305 <filter>'mlocarna_results' in outputs</filter>
306 </data>
307 </xml>
308
309 <xml name="citations">
310 <citations>
311 <citation
312 type="doi">10.1371/journal.pcbi.0030065</citation>
313 <citation type="doi">10.1261/rna.029041.111</citation>
314 <citation type="doi">10.1093/bioinformatics/btv185</citation>
315 <citation type="doi">10.1186/s12859-014-0404-0</citation>
316 </citations>
317 </xml>
318
319
320
321 </macros>
322