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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 14:29:23 +0000
parents c5f150d2686f
children
comparison
equal deleted inserted replaced
1:53583f715a8c 2:535f2e41d4f7
1 <tool id="locarna_pairwise_p" name="LocARNA Pairwise Probability Aligner" version="@VERSION@.0"> 1 <tool id="locarna_pairwise_p" name="LocARNA Pairwise Probability Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P) 3 Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P)
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
13 13
14 <expand macro="version" /> 14 <expand macro="version" />
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
17 locarna_p 17 locarna_p
18 18
19 '$inputA' 19 '$inputA'
20 '$inputB' 20 '$inputB'
21 21
22 --width 60
23
24 @SCORING_ARGS@ 22 @SCORING_ARGS@
25 23
26 @FOLDING_ARGS@ 24 @FOLDING_ARGS@
27 25
28 @HEURISTIC_ARGS@ 26 @HEURISTIC_ARGS@
29 #if float($Heuristics.pf_scale) != 1.0 27 #if float($Heuristics.pf_scale) != 1.0
30 --pf-scale $Heuristics.pf_scale 28 --pf-scale $Heuristics.pf_scale
31 #end if 29 #end if
32 30
33 ## -------------------- other parameters 31 ## -------------------- other parameters
34 32 @CONSTRAINT_ARGS_WOLP@
35 #if $Constraints.maxBPspan != -1
36 --maxBPspan $Constraints.maxBPspan
37 #end if
38
39 $Constraints.ignore_constraints
40 33
41 ## -------------------- probability parameters 34 ## -------------------- probability parameters
42 $Probabilities.include_am_in_bm 35 $Probabilities.include_am_in_bm
43 #if float($Probabilities.min_bm_prob) != 0.0005 36 #if float($Probabilities.min_bm_prob) != 0.0005
44 --min-bm-prob $Probabilities.min_bm_prob 37 --min-bm-prob $Probabilities.min_bm_prob
67 /> 60 />
68 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" 61 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
69 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format" 62 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
70 /> 63 />
71 64
72 <param name="outputs" type="select" display="checkboxes" multiple="True" 65 <param name="outputs" type="select" display="checkboxes" multiple="true"
73 label="Output options"> 66 label="Output options">
74 <option value="base_match_probs" selected="True"> 67 <option value="base_match_probs" selected="true">
75 Output base match probabilities</option> 68 Output base match probabilities</option>
76 <option value="arc_match_probs" selected="True"> 69 <option value="arc_match_probs" selected="true">
77 Output arc match probabilities</option> 70 Output arc match probabilities</option>
78 </param> 71 </param>
79 72
80 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> 73 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
81 <option value="--quiet">Don't report standard 74 <option value="--quiet">Don't report standard
83 <option value="">Non verbose</option> 76 <option value="">Non verbose</option>
84 <option value="--verbose">Verbose</option> 77 <option value="--verbose">Verbose</option>
85 </param> 78 </param>
86 79
87 <section name="Probabilities" title="Probability parameters"> 80 <section name="Probabilities" title="Probability parameters">
88 <param name="include_am_in_bm" argument="include-am-in-bm" 81 <param argument="--include-am-in-bm"
89 type="boolean" 82 type="boolean"
90 truevalue="--include-am-in-bm" falsevalue="" 83 truevalue="--include-am-in-bm" falsevalue=""
91 label="Include arc match cases in computation of base match probabilities" /> 84 label="Include arc match cases in computation of base match probabilities" />
92 <param name="min_bm_prob" argument="min-bm-prob" 85 <param argument="--min-bm-prob"
93 type="float" 86 type="float"
94 value="0.0005" min="0.0" max="1.0" 87 value="0.0005" min="0.0" max="1.0"
95 label="Minimal base match probability" 88 label="Minimal base match probability"
96 /> 89 />
97 <param name="min_am_prob" argument="min-am-prob" 90 <param argument="--min-am-prob"
98 type="float" 91 type="float"
99 value="0.0005" min="0.0" max="1.0" 92 value="0.0005" min="0.0" max="1.0"
100 label="Minimal arc match probability" 93 label="Minimal arc match probability"
101 /> 94 />
102 </section> 95 </section>
105 <expand macro="common_scoring_parameters" /> 98 <expand macro="common_scoring_parameters" />
106 </section> 99 </section>
107 100
108 <section name="Folding" title="RNA folding parameters"> 101 <section name="Folding" title="RNA folding parameters">
109 <expand macro="common_folding_parameters" /> 102 <expand macro="common_folding_parameters" />
110 <expand macro="alifold_consensus_parameter" />
111 <param name="consensus_structure" type="select" label="Consensus structure type"
112 help="Type of consensus structures written to screen and stockholm output"
113 >
114 <!-- <option value="mea">mea</option>-->
115 <option value="none">none</option>
116 <option value="alifold">alifold</option>
117 </param>
118 </section> 103 </section>
119 104
120 <section name="Heuristics" title="Heuristic parameters"> 105 <section name="Heuristics" title="Heuristic parameters">
121 <expand macro="common_heuristic_parameters" /> 106 <expand macro="common_heuristic_parameters" />
122 <expand macro="max_diff_parameters_aln" /> 107 <expand macro="max_diff_parameters_aln" />
123 <param name="pf_scale" argument="pf-scale" 108 <param argument="--pf-scale"
124 type="float" value="1.0" 109 type="float" value="1.0"
125 label="Scaling of the partition function." 110 label="Scaling of the partition function."
126 help="Use (only) if standard scaling overflows." /> 111 help="Use (only) if standard scaling overflows." />
127 </section> 112 </section>
128 113
129 <section name="Constraints" title="Constraint parameters"> 114 <section name="Constraints" title="Constraint parameters">
130 <expand macro="common_constraint_parameters" /> 115 <expand macro="common_constraint_parameters_woLP" />
131 </section> 116 </section>
132 117
133 </inputs> 118 </inputs>
134 119
135 <outputs> 120 <outputs>
141 <filter>'arc_match_probs' in outputs</filter> 126 <filter>'arc_match_probs' in outputs</filter>
142 </data> 127 </data>
143 </outputs> 128 </outputs>
144 129
145 <tests> 130 <tests>
146 <test> 131 <test expect_num_outputs="2">
147 <param name="inputA" value="tRNA_2-1.fa" /> 132 <param name="inputA" value="tRNA_2-1.fa" />
148 <param name="inputB" value="tRNA_2-2.fa" /> 133 <param name="inputB" value="tRNA_2-2.fa" />
149 <param name="outputs" value="arc_match_probs,base_match_probs"/> 134 <param name="outputs" value="arc_match_probs,base_match_probs"/>
150 <param name="min_bm_prob" value="0.01" /> 135 <param name="min_bm_prob" value="0.01" />
151 <param name="min_am_prob" value="0.01" /> 136 <param name="min_am_prob" value="0.01" />