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comparison locarna_multiple.xml @ 4:6e20ad2c8752 draft default tip

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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 18:52:41 +0000
parents 7554c0df9139
children
comparison
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3:7554c0df9139 4:6e20ad2c8752
1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 Multiple Alignment and Folding of RNAs (mlocarna) 3 Multiple Alignment and Folding of RNAs (mlocarna)
4 </description> 4 </description>
5
6 <macros> 5 <macros>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
8 </macros> 7 </macros>
9 8 <expand macro="requirements"/>
10 <expand macro="requirements" /> 9 <expand macro="stdio"/>
11
12 <expand macro="stdio" />
13
14 <expand macro="version" /> 10 <expand macro="version" />
15
16 <command><![CDATA[ 11 <command><![CDATA[
17 mlocarna 12 mlocarna
18
19 '$input_data' 13 '$input_data'
20 #if 'stockholm' in str($outputs).split(","): 14 #if 'stockholm' in str($outputs).split(","):
21 --stockholm 15 --stockholm
22 #end if 16 #end if
23 17
24 --tgtdir mlocarna_results 18 --tgtdir mlocarna_results
25 ## maybe reenable later? see https://github.com/s-will/LocARNA/issues/77 19 ## maybe reenable later? see https://github.com/s-will/LocARNA/issues/77
26 ## --width 60 20 ## --width 60
27 21
28 ## -------------------- alignment mode and specific options 22 ## -------------------- alignment mode and specific option--------- #
29 #
30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna" 23 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
31 $alignment_mode.free_endgaps 24 $alignment_mode.free_endgaps
32 #elif str($alignment_mode.alignment_mode_selector) == "local_locarna" 25 #elif str($alignment_mode.alignment_mode_selector) == "local_locarna"
33 --sequ-local on 26 --sequ-local on
34 #elif str($alignment_mode.alignment_mode_selector) == "probabilistic" 27 #elif str($alignment_mode.alignment_mode_selector) == "probabilistic"
76 <param name="input_data_type_selector" type="select" label="Input type"> 69 <param name="input_data_type_selector" type="select" label="Input type">
77 <option value="fasta">Fasta input (strict)</option> 70 <option value="fasta">Fasta input (strict)</option>
78 <option value="text">Fasta-like input with LocARNA constraints</option> 71 <option value="text">Fasta-like input with LocARNA constraints</option>
79 </param> 72 </param>
80 <when value="fasta"> 73 <when value="fasta">
81 <param name="input_data" type="data" format="fasta" label="Sequence input" 74 <param name="input_data" type="data" format="fasta" label="Sequence input" help="Sequence input in pure fasta format"/>
82 help="Sequence input in pure fasta format"
83 />
84 </when> 75 </when>
85 <when value="text"> 76 <when value="text">
86 <param name="input_data" type="data" format="text" label="Sequence input" 77 <param name="input_data" type="data" format="text" label="Sequence input" help="Sequence input in fasta format with locarna-specific extensions"/>
87 help="Sequence input in fasta format with locarna-specific extensions"
88 />
89 </when> 78 </when>
90 </conditional> 79 </conditional>
91 <conditional name="alignment_mode"> 80 <conditional name="alignment_mode">
92 <param name="alignment_mode_selector" type="select" label="Alignment mode" 81 <param name="alignment_mode_selector" type="select" label="Alignment mode" help="Note that local alignment mode usually requires to turn off the 'max-diff' heuristic (maximal difference for alignment traces).">
93 help="Note that local alignment mode usually requires to turn off
94 the 'max-diff' heuristic (maximal difference for alignment traces)."
95 >
96 <option value="global_locarna">Global alignment (LocARNA)</option> 82 <option value="global_locarna">Global alignment (LocARNA)</option>
97 <option value="local_locarna">Local alignment (LocARNA)</option> 83 <option value="local_locarna">Local alignment (LocARNA)</option>
98 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option> 84 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
99 <option value="sparse">Global fast alignment (SPARSE)</option> 85 <option value="sparse">Global fast alignment (SPARSE)</option>
100 </param> 86 </param>
101 <when value="global_locarna"> 87 <when value="global_locarna">
102 <param name="free_endgaps" type="select" label="Free endgaps" 88 <param name="free_endgaps" type="select" label="Free endgaps" help="Specify whether gaps at the ends (all, 5', or 3' ends)of the sequences should be penalized or allowed for free.">
103 help="Specify whether gaps at the ends (all, 5', or 3' ends)
104 of the sequences should be penalized or allowed for free.">
105 <option value="">No free endgaps</option> 89 <option value="">No free endgaps</option>
106 <option value="--free-endgaps">Free endgaps</option> 90 <option value="--free-endgaps">Free endgaps</option>
107 <option value="--free-endgaps-5">Free endgaps, only 5'</option> 91 <option value="--free-endgaps-5">Free endgaps, only 5'</option>
108 <option value="--free-endgaps-3">Free endgaps, only 3'</option> 92 <option value="--free-endgaps-3">Free endgaps, only 3'</option>
109 </param> 93 </param>
110 </when> 94 </when>
111 <when value="local_locarna"> 95 <when value="local_locarna">
112 </when> 96 </when>
113 <when value="probabilistic"> 97 <when value="probabilistic">
114 <param name="consistency_transformation" type="boolean" 98 <param name="consistency_transformation" type="boolean" truevalue="--consistency-transformation" falsevalue="" checked="true" label="Consistency transformation" help="--consistency-transformation"/>
115 truevalue="--consistency-transformation" falsevalue="" 99 <param name="iterate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Iterative refinement" help="--iterate"/>
116 checked="true" label="Consistency transformation" 100 <param name="iterations" type="integer" value="1" label="Number of refinement iterations" help="--iterations num"/>
117 help="--consistency-transformation" />
118 <param name="iterate" type="boolean"
119 truevalue="true" falsevalue="false"
120 checked="false" label="Iterative refinement"
121 help="--iterate" />
122 <param name="iterations" type="integer"
123 value="1" label="Number of refinement iterations"
124 help="--iterations num" />
125 </when> 101 </when>
126 <when value="sparse"> 102 <when value="sparse">
127 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE"> 103 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
128 <expand macro="common_heuristic_parameters_sparse" /> 104 <expand macro="common_heuristic_parameters_sparse" />
129 </section> 105 </section>