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comparison locarna_multiple.xml @ 1:a5a2d3cefce1 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 16:48:50 -0500
parents 8414fea2a6fd
children 94b0468f0db8
comparison
equal deleted inserted replaced
0:8414fea2a6fd 1:a5a2d3cefce1
1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner (mlocarna)" version="@VERSION@.0"> 1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1">
2 <description> 2 <description>
3 Multiple Alignment and Folding of RNAs 3 Multiple Alignment and Folding of RNAs (mlocarna)
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
23 23
24 --tgtdir mlocarna_results 24 --tgtdir mlocarna_results
25 --width 60 25 --width 60
26 26
27 ## -------------------- alignment mode and specific options 27 ## -------------------- alignment mode and specific options
28 28 #
29 #if str($alignment_mode.alignment_mode_selector) == "global_locarna" 29 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
30 $alignment_mode.free_endgaps 30 $alignment_mode.free_endgaps
31 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna" 31 #elif str($alignment_mode.alignment_mode_selector) == "local_locarna"
32 --sequ-local on 32 --sequ-local on
33 #else if str($alignment_mode.alignment_mode_selector) == "probabilistic" 33 #elif str($alignment_mode.alignment_mode_selector) == "probabilistic"
34 --probabilistic 34 --probabilistic
35 $alignment_mode.consistency_transformation 35 $alignment_mode.consistency_transformation
36 36
37 #if str($alignment_mode.iterate) == "true" 37 #if str($alignment_mode.iterate) == "true"
38 --iterate 38 --iterate
39 --iterations $alignment_mode.iterations 39 --iterations $alignment_mode.iterations
40 #end if 40 #end if
41 #else if str($alignment_mode.alignment_mode_selector) == "sparse" 41 #elif str($alignment_mode.alignment_mode_selector) == "sparse"
42 --sparse 42 --sparse
43 #end if 43 #end if
44 44
45 ## -------------------- scoring parameters 45 @SCORING_ARGS@
46 46
47 --indel $Scoring.indel 47 @FOLDING_ARGS@
48 --indel-opening $Scoring.indel_opening
49 --struct-weight $Scoring.struct_weight
50 --tau $Scoring.tau
51
52 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
53 --match $Scoring.sequence_score.match
54 --mismatch $Scoring.sequence_score.mismatch
55 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
56 --use-ribosum true
57 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
58 --ribofit true
59 #end if
60
61 ## -------------------- folding parameters
62
63 #if $Folding.plfold_span>=0 48 #if $Folding.plfold_span>=0
64 --plfold-span $Folding.plfold_span 49 --plfold-span $Folding.plfold_span
65 --plfold-winsize $Folding.plfold_winsize 50 --plfold-winsize $Folding.plfold_winsize
66 #end if 51 #end if
67
68 #if float($Folding.rnafold_temperature) != 37.0
69 --rnafold-temperature $Folding.rnafold_temperature
70 #end if
71
72 $Folding.alifold_consensus_dp 52 $Folding.alifold_consensus_dp
73 53
74 ## -------------------- heuristic parameters 54 @HEURISTIC_ARGS@
75 55
76 -p $Heuristics.min_prob 56 @CONSTRAINT_ARGS@
77 --max-diff-am $Heuristics.max_diff_am 57 #if str($Constraints.bed_anchors.bed_anchors_selector) == "yes"
78 --max-diff $Heuristics.max_diff 58 --anchor-constraints $Constraints.bed_anchors.bed_anchors_file
79 --max-diff-at-am $Heuristics.max_diff_at_am 59 #end if
80 --max-bps-length-ratio $Heuristics.max_bps_length_ratio 60
81 61 @STDOUT_ARGS@
82
83 ## -------------------- other parameters
84
85 #if str($Constraint.bed_anchors.bed_anchors_selector) == "yes"
86 --anchor-constraints $Constraint.bed_anchors.bed_anchors_file
87 #end if
88
89 $Constraint.lonely_pairs
90
91 #if $Constraint.maxBPspan != -1
92 --maxBPspan $Constraint.maxBPspan
93 #end if
94
95 $Constraint.ignore_constraints
96
97 $stdout_verbosity
98
99 #if str($stdout_verbosity) != "--quiet":
100 > '$stdout'
101 #end if
102 62
103 #if 'clustal_strict' in str($outputs).split(",") 63 #if 'clustal_strict' in str($outputs).split(",")
104 && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln 64 && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
105 #end if 65 #end if
106 66
194 <expand macro="alifold_consensus_parameter" /> 154 <expand macro="alifold_consensus_parameter" />
195 </section> 155 </section>
196 156
197 <section name="Heuristics" title="Heuristic parameters"> 157 <section name="Heuristics" title="Heuristic parameters">
198 <expand macro="common_heuristic_parameters" /> 158 <expand macro="common_heuristic_parameters" />
199 </section> 159 <expand macro="max_diff_parameters_aln" />
200 160 </section>
201 <section name="Constraint" title="Constraint parameters"> 161
162 <section name="Constraints" title="Constraint parameters">
202 <expand macro="bed_anchors" /> 163 <expand macro="bed_anchors" />
203 <expand macro="constraints" /> 164 <expand macro="common_constraint_parameters" />
204 </section> 165 </section>
205 </inputs> 166 </inputs>
206 167
207 <outputs> 168 <outputs>
208 <expand macro="common_outputs" /> 169 <expand macro="mlocarna_outputs" />
209 </outputs> 170 </outputs>
210 171
211 <tests> 172 <tests>
212 <test> 173 <test>
213 <param name="input_data" value="archaea.fa" /> 174 <param name="input_data" value="archaea.fa" />
214 <param name="stdout_verbosity" value="" /> 175 <param name="stdout_verbosity" value="" />
176 <param name="max_diff_mode_selector" value="max-diff" />
177 <param name="max_diff" value="20" />
215 <output name="stdout" file="archaea-default.stdout" /> 178 <output name="stdout" file="archaea-default.stdout" />
216 </test> 179 </test>
217 <test> 180 <test>
218 <param name="input_data" value="haca.snoRNA.fa" /> 181 <param name="input_data" value="haca.snoRNA.fa" />
219 <param name="stdout_verbosity" value="" /> 182 <param name="stdout_verbosity" value="" />
223 <param name="input_data" value="archaea.fa" /> 186 <param name="input_data" value="archaea.fa" />
224 <param name="stdout_verbosity" value="" /> 187 <param name="stdout_verbosity" value="" />
225 <param name="outputs" value="clustal" /> 188 <param name="outputs" value="clustal" />
226 <param name="alignment_mode_selector" value="probabilistic" /> 189 <param name="alignment_mode_selector" value="probabilistic" />
227 <output name="clustal" file="archaea-probabilistic.aln" /> 190 <output name="clustal" file="archaea-probabilistic.aln" />
191 </test>
192 <test>
193 <param name="input_data" value="archaea.fa" />
194 <param name="stdout_verbosity" value="" />
195 <param name="outputs" value="clustal" />
196 <param name="max_diff_mode_selector" value="max-diff-aln" />
197 <param name="max_diff_aln" value="archaea-ref.aln" />
198 <param name="max_diff" value="2" />
199 <output name="clustal" file="archaea-ref_result.aln" />
228 </test> 200 </test>
229 </tests> 201 </tests>
230 202
231 <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs** 203 <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs**
232 204