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comparison macros.xml @ 1:b06dc2bb3716 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 16:49:33 -0500
parents 6a79a086fa50
children 433601e9f132
comparison
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0:6a79a086fa50 1:b06dc2bb3716
23 23
24 <xml name="bed_anchors"> 24 <xml name="bed_anchors">
25 <conditional name="bed_anchors"> 25 <conditional name="bed_anchors">
26 <param name="bed_anchors_selector" type="select" label="Anchor constraints" 26 <param name="bed_anchors_selector" type="select" label="Anchor constraints"
27 help="Anchor constraints in bed format specify positions of 27 help="Anchor constraints in bed format specify positions of
28 named anchor regions per sequence. The sequence names 28 named anchor regions per sequence. The sequence names
29 ('contig' names have to correspond to the fasta input 29 ('contig' names have to correspond to the fasta input
30 sequence names. Anchor names must be unique per sequence 30 sequence names. Anchor names must be unique per sequence
31 and regions of the same name for different sequences 31 and regions of the same name for different sequences
32 must have the same length. This constrains the alignment 32 must have the same length. This constrains the alignment
33 to align all regions of the same name."> 33 to align all regions of the same name.">
34 <option value="no">Don't load anchor constraints from bed file</option> 34 <option value="no">Don't load anchor constraints from
35 <option value="yes">Load anchor constraints from bed file</option> 35 bed file</option>
36 <option value="yes">Load anchor constraints from bed
37 file</option>
36 </param> 38 </param>
37 <when value="no" /> 39 <when value="no" />
38 <when value="yes"> 40 <when value="yes">
39 <param name="bed_anchors_file" type="data" format="tabular" 41 <param name="bed_anchors_file" type="data" format="tabular"
40 label="Anchor constraint specification in bed format" 42 label="Anchor constraint specification in bed format"
89 <param name="rnafold_temperature" argument="rnafold-temperature" 91 <param name="rnafold_temperature" argument="rnafold-temperature"
90 type="float" value="37.0" min="10" max="50" 92 type="float" value="37.0" min="10" max="50"
91 label="Temperature for RNAfold (RNAfold's -T option)" /> 93 label="Temperature for RNAfold (RNAfold's -T option)" />
92 </xml> 94 </xml>
93 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
94 <xml name="common_heuristic_parameters"> 219 <xml name="common_heuristic_parameters">
95 <param name="min_prob" argument="min-prob" type="float" value="0.0005" 220 <param name="min_prob" argument="min-prob" type="float" value="0.0005"
96 min="0.0" max="0.2" 221 min="0.0" max="0.2"
97 label="Minimal / cutoff probability" /> 222 label="Minimal / cutoff probability" />
98 223
99 <param name="max_diff_am" argument="max-diff-am" 224 <param name="max_diff_am" argument="max-diff-am"
100 type="integer" value="30" 225 type="integer" value="30"
101 min="-1" max="300" 226 min="-1" max="300"
102 label="Maximal difference for sizes of matched arcs (-1=off)" /> 227 label="Maximal difference for sizes of matched arcs (-1=off)" />
103
104 <param name="max_diff" argument="max-diff" type="integer"
105 value="60" min="-1" max="300"
106 label="Maximal difference for alignment traces (-1=off)" />
107
108 <param name="max_diff_at_am" argument="max-diff-am" type="integer"
109 value="-1" min="-1" max="300"
110 label="Maximal difference for alignment traces, only at arc match positions" />
111 228
112 <param name="max_bps_length_ratio" argument="max-bps-length-ratio" 229 <param name="max_bps_length_ratio" argument="max-bps-length-ratio"
113 type="float" value="0.0" min="0.0" max="1.0" 230 type="float" value="0.0" min="0.0" max="10.0"
114 label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" /> 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" />
115 </xml> 256 </xml>
116 257
117 <xml name="alifold_consensus_parameter"> 258 <xml name="alifold_consensus_parameter">
118 <param name="alifold_consensus_dp" argument="alifold-consensus-dp" 259 <param name="alifold_consensus_dp" argument="alifold-consensus-dp"
119 type="boolean" checked="false" 260 type="boolean" checked="False"
120 truevalue="--alifold-consensus-dp" falsevalue="" 261 truevalue="--alifold-consensus-dp" falsevalue=""
121 label="Compute consensus dot plot by alifold" /> 262 label="Compute consensus dot plot by alifold" />
122 </xml> 263 </xml>
123 264
124 <xml name="constraints"> 265 <xml name="common_constraint_parameters">
125 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" 266 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP"
126 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> 267 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
127 <param name="maxBPspan" argument="--maxBPspan" 268 <param name="maxBPspan" argument="--maxBPspan"
128 type="integer" value="-1" min="-1" max="400" 269 type="integer" value="-1" min="-1" max="400"
129 label="Maximum basepair span by RNAfold; -1 for arbitrary span" /> 270 label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
131 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue="" 272 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
132 help="Ignore all anchor and structure constraints given 273 help="Ignore all anchor and structure constraints given
133 in the fasta(-ish) input." /> 274 in the fasta(-ish) input." />
134 </xml> 275 </xml>
135 276
136 <xml name="common_other_parameters"> 277 <xml name="standard_outupt">
137 </xml>
138
139 <xml name="common_outputs">
140 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> 278 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
141 <filter>stdout_verbosity != '--quiet'</filter> 279 <filter>stdout_verbosity != '--quiet'</filter>
142 </data> 280 </data>
281 </xml>
282
283 <xml name="mlocarna_outputs">
284 <expand macro="standard_outupt" />
143 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" 285 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
144 label="${tool.name} alignment (annotated clustal) on ${on_string}"> 286 label="${tool.name} alignment (annotated clustal) on ${on_string}">
145 <filter>'clustal' in outputs</filter> 287 <filter>'clustal' in outputs</filter>
146 </data> 288 </data>
147 <data format="clustal" name="clustal_strict" 289 <data format="clustal" name="clustal_strict"
167 <xml name="citations"> 309 <xml name="citations">
168 <citations> 310 <citations>
169 <citation 311 <citation
170 type="doi">10.1371/journal.pcbi.0030065</citation> 312 type="doi">10.1371/journal.pcbi.0030065</citation>
171 <citation type="doi">10.1261/rna.029041.111</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>
172 </citations> 316 </citations>
173 </xml> 317 </xml>
174 318
175 319
176 320