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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
author bgruening
date Mon, 19 Aug 2024 18:52:22 +0000
parents 535f2e41d4f7
children
comparison
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2:535f2e41d4f7 3:a1c9c960cdd5
1 <tool id="locarna_pairwise_p" name="LocARNA Pairwise Probability Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 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
6 <macros> 5 <macros>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
8 </macros> 7 </macros>
9
10 <expand macro="requirements" /> 8 <expand macro="requirements" />
11
12 <expand macro="stdio" /> 9 <expand macro="stdio" />
13
14 <expand macro="version" /> 10 <expand macro="version" />
15
16 <command><![CDATA[ 11 <command><![CDATA[
17 locarna_p 12 locarna_p
18
19 '$inputA' 13 '$inputA'
20 '$inputB' 14 '$inputB'
21 15
22 @SCORING_ARGS@ 16 @SCORING_ARGS@
23 17
26 @HEURISTIC_ARGS@ 20 @HEURISTIC_ARGS@
27 #if float($Heuristics.pf_scale) != 1.0 21 #if float($Heuristics.pf_scale) != 1.0
28 --pf-scale $Heuristics.pf_scale 22 --pf-scale $Heuristics.pf_scale
29 #end if 23 #end if
30 24
31 ## -------------------- other parameters 25 ## -------------------- other parameters ----------------#
32 @CONSTRAINT_ARGS_WOLP@ 26 @CONSTRAINT_ARGS_WOLP@
33 27
34 ## -------------------- probability parameters 28 ## -------------------- probability parameters ----------------#
35 $Probabilities.include_am_in_bm 29 $Probabilities.include_am_in_bm
36 #if float($Probabilities.min_bm_prob) != 0.0005 30 #if float($Probabilities.min_bm_prob) != 0.0005
37 --min-bm-prob $Probabilities.min_bm_prob 31 --min-bm-prob $Probabilities.min_bm_prob
38 #end if 32 #end if
39 #if float($Probabilities.min_am_prob) != 0.0005 33 #if float($Probabilities.min_am_prob) != 0.0005
40 --min-am-prob $Probabilities.min_am_prob 34 --min-am-prob $Probabilities.min_am_prob
41 #end if 35 #end if
42 36
43 ## -------------------- output 37 ## -------------------- output ----------------#
44 38
45 #if not $arc_match_probs is None 39 #if not $arc_match_probs is None
46 --write-arcmatch-probs=$arc_match_probs 40 --write-arcmatch-probs=$arc_match_probs
47 #end if 41 #end if
48 42
53 @STDOUT_ARGS@ 47 @STDOUT_ARGS@
54 48
55 ]]></command> 49 ]]></command>
56 50
57 <inputs> 51 <inputs>
58 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" 52 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
59 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format" 53 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
60 /> 54 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
61 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" 55 <option value="base_match_probs" selected="true">Output base match probabilities</option>
62 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format" 56 <option value="arc_match_probs" selected="true">Output arc match probabilities</option>
63 />
64
65 <param name="outputs" type="select" display="checkboxes" multiple="true"
66 label="Output options">
67 <option value="base_match_probs" selected="true">
68 Output base match probabilities</option>
69 <option value="arc_match_probs" selected="true">
70 Output arc match probabilities</option>
71 </param> 57 </param>
72
73 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> 58 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
74 <option value="--quiet">Don't report standard 59 <option value="--quiet">Don't report standard output</option>
75 output</option>
76 <option value="">Non verbose</option> 60 <option value="">Non verbose</option>
77 <option value="--verbose">Verbose</option> 61 <option value="--verbose">Verbose</option>
78 </param> 62 </param>
79
80 <section name="Probabilities" title="Probability parameters"> 63 <section name="Probabilities" title="Probability parameters">
81 <param argument="--include-am-in-bm" 64 <param argument="--include-am-in-bm" type="boolean" truevalue="--include-am-in-bm" falsevalue="" label="Include arc match cases in computation of base match probabilities" />
82 type="boolean" 65 <param argument="--min-bm-prob" type="float" value="0.0005" min="0.0" max="1.0" label="Minimal base match probability"/>
83 truevalue="--include-am-in-bm" falsevalue="" 66 <param argument="--min-am-prob" type="float" value="0.0005" min="0.0" max="1.0" label="Minimal arc match probability"/>
84 label="Include arc match cases in computation of base match probabilities" />
85 <param argument="--min-bm-prob"
86 type="float"
87 value="0.0005" min="0.0" max="1.0"
88 label="Minimal base match probability"
89 />
90 <param argument="--min-am-prob"
91 type="float"
92 value="0.0005" min="0.0" max="1.0"
93 label="Minimal arc match probability"
94 />
95 </section> 67 </section>
96 68
97 <section name="Scoring" title="Scoring parameters"> 69 <section name="Scoring" title="Scoring parameters">
98 <expand macro="common_scoring_parameters" /> 70 <expand macro="common_scoring_parameters" />
99 </section> 71 </section>
103 </section> 75 </section>
104 76
105 <section name="Heuristics" title="Heuristic parameters"> 77 <section name="Heuristics" title="Heuristic parameters">
106 <expand macro="common_heuristic_parameters" /> 78 <expand macro="common_heuristic_parameters" />
107 <expand macro="max_diff_parameters_aln" /> 79 <expand macro="max_diff_parameters_aln" />
108 <param argument="--pf-scale" 80 <param argument="--pf-scale" type="float" value="1.0" label="Scaling of the partition function." help="Use (only) if standard scaling overflows." />
109 type="float" value="1.0"
110 label="Scaling of the partition function."
111 help="Use (only) if standard scaling overflows." />
112 </section> 81 </section>
113 82
114 <section name="Constraints" title="Constraint parameters"> 83 <section name="Constraints" title="Constraint parameters">
115 <expand macro="common_constraint_parameters_woLP" /> 84 <expand macro="common_constraint_parameters_woLP" />
116 </section> 85 </section>
117
118 </inputs> 86 </inputs>
119 87
120 <outputs> 88 <outputs>
121 <expand macro="standard_outupt" /> 89 <expand macro="standard_outupt" />
122 <data format="table" name="base_match_probs" label="${tool.name} base match probabilties on ${on_string}"> 90 <data format="table" name="base_match_probs" label="${tool.name} base match probabilties on ${on_string}">