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comparison locarna_pairwise.xml @ 4:4839df2b2f6b 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 18:52:50 +0000
parents f3f08a777c10
children
comparison
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3:f3f08a777c10 4:4839df2b2f6b
1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse) 3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
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 #if str($alignment_mode.alignment_mode_selector) == "sparse" 12 #if str($alignment_mode.alignment_mode_selector) == "sparse"
18 sparse 13 sparse
19 #else 14 #else
20 locarna 15 locarna
23 '$inputA' 18 '$inputA'
24 '$inputB' 19 '$inputB'
25 20
26 ## --width 60 21 ## --width 60
27 22
28 ## -------------------- alignment mode and specific options 23 ## -------------------- alignment mode and specific options ----------------#
29 24
30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna" 25 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
31 #if str($alignment_mode.free_endgaps) != "----" 26 #if str($alignment_mode.free_endgaps) != "----"
32 --free-endgaps $alignment_mode.free_endgaps 27 --free-endgaps $alignment_mode.free_endgaps
33 #end if 28 #end if
52 @HEURISTIC_SPARSE_ARGS@ 47 @HEURISTIC_SPARSE_ARGS@
53 #end if 48 #end if
54 49
55 @CONSTRAINT_ARGS@ 50 @CONSTRAINT_ARGS@
56 51
57 ## -------------------- output 52 ## -------------------- output ----------------#
58 53
59 #if 'stockholm' in str($outputs).split(",") 54 #if 'stockholm' in str($outputs).split(",")
60 --stockholm '$stockholm' 55 --stockholm '$stockholm'
61 #end if 56 #end if
62 #if 'clustal' in str($outputs).split(",") 57 #if 'clustal' in str($outputs).split(",")
81 #end if 76 #end if
82 77
83 ]]></command> 78 ]]></command>
84 79
85 <inputs> 80 <inputs>
86 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" 81 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
87 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format" 82 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
88 />
89 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
90 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
91 />
92 <conditional name="alignment_mode"> 83 <conditional name="alignment_mode">
93 <param name="alignment_mode_selector" type="select" label="Alignment mode" 84 <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).">
94 help="Note that local alignment mode usually requires to turn off 85 <option value="global_locarna">Global alignment(LocARNA)</option>
95 the 'max-diff' heuristic (maximal difference for alignment traces)."
96 >
97 <option value="global_locarna">Global alignment
98 (LocARNA)</option>
99 <option value="local_locarna">Local alignment (LocARNA)</option> 86 <option value="local_locarna">Local alignment (LocARNA)</option>
100 <option value="sparse">Global fast alignment (SPARSE)</option> 87 <option value="sparse">Global fast alignment (SPARSE)</option>
101 <option value="structure_sequence_local_locarna"> 88 <option value="structure_sequence_local_locarna">Structure and sequence local alignment (LocARNA)</option>
102 Structure and sequence local alignment (LocARNA) 89 <option value="structure_local_locarna">Structure local, sequence global alignment (LocARNA)</option>
103 </option>
104 <option value="structure_local_locarna">
105 Structure local, sequence global alignment (LocARNA)
106 </option>
107 </param> 90 </param>
108 <when value="global_locarna"> 91 <when value="global_locarna">
109 <param name="free_endgaps" type="select" label="Free endgaps" 92 <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.">
110 help="Specify whether gaps at the ends (all, 5', or 3' ends)
111 of the sequences should be penalized or allowed for free.">
112 <option value="----">None</option> 93 <option value="----">None</option>
113 <option value="++++">All</option> 94 <option value="++++">All</option>
114 <option value="+-+-">5' ends</option> 95 <option value="+-+-">5' ends</option>
115 <option value="-+-+">3' ends</option> 96 <option value="-+-+">3' ends</option>
116 <option value="++--">first sequence</option> 97 <option value="++--">first sequence</option>
125 </when> 106 </when>
126 <when value="sparse"> 107 <when value="sparse">
127 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE"> 108 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
128 <expand macro="common_heuristic_parameters_sparse" /> 109 <expand macro="common_heuristic_parameters_sparse" />
129 </section> 110 </section>
130
131 </when> 111 </when>
132 112
133 <when value="structure_sequence_local_locarna" /> 113 <when value="structure_sequence_local_locarna" />
134 <when value="structure_local_locarna" /> 114 <when value="structure_local_locarna" />
135 </conditional> 115 </conditional>
136 116
137 <param name="outputs" type="select" display="checkboxes" multiple="true" 117 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
138 label="Output options"> 118 <option value="clustal_strict" selected="true">Output alignment in ClustalW format</option>
139 <option value="clustal_strict" selected="true">Output alignment 119 <option value="clustal" selected="false">Output alignment in constraint-annotated ClustalW format</option>
140 in ClustalW format</option> 120 <option value="stockholm" selected="false">Output alignment in Stockholm format</option>
141 <option value="clustal" selected="false">Output alignment 121 <option value="pp" selected="false">Output alignment in LocARNA's PP 2.0 format</option>
142 in constraint-annotated ClustalW format</option>
143 <option value="stockholm" selected="false">Output
144 alignment in Stockholm format</option>
145 <option value="pp" selected="false">Output
146 alignment in LocARNA's PP 2.0 format</option>
147 </param> 122 </param>
148 123
149 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> 124 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
150 <option value="--quiet">Don't report standard 125 <option value="--quiet">Don't report standard output</option>
151 output</option>
152 <option value="">Non verbose</option> 126 <option value="">Non verbose</option>
153 <option value="--verbose">Verbose</option> 127 <option value="--verbose">Verbose</option>
154 </param> 128 </param>
155 129
156 <section name="Scoring" title="Scoring parameters"> 130 <section name="Scoring" title="Scoring parameters">
158 </section> 132 </section>
159 133
160 <section name="Folding" title="RNA folding parameters"> 134 <section name="Folding" title="RNA folding parameters">
161 <expand macro="common_folding_parameters" /> 135 <expand macro="common_folding_parameters" />
162 <expand macro="alifold_consensus_parameter" /> 136 <expand macro="alifold_consensus_parameter" />
163 <param name="consensus_structure" type="select" label="Consensus structure type" 137 <param name="consensus_structure" type="select" label="Consensus structure type" help="Type of consensus structures written to screen and stockholm output">
164 help="Type of consensus structures written to screen and stockholm output"
165 >
166 <!-- <option value="mea">mea</option>--> 138 <!-- <option value="mea">mea</option>-->
167 <option value="none">none</option> 139 <option value="none">none</option>
168 <option value="alifold">alifold</option> 140 <option value="alifold">alifold</option>
169 </param> 141 </param>
170 </section> 142 </section>
179 </section> 151 </section>
180 </inputs> 152 </inputs>
181 153
182 <outputs> 154 <outputs>
183 <expand macro="standard_outupt" /> 155 <expand macro="standard_outupt" />
184 <data format="clustal" name="clustal" 156 <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: alignment (annotated clustal)">
185 label="${tool.name} on ${on_string}: alignment (annotated clustal)">
186 <filter>'clustal' in outputs</filter> 157 <filter>'clustal' in outputs</filter>
187 </data> 158 </data>
188 <data format="clustal" name="clustal_strict" 159 <data format="clustal" name="clustal_strict" label="${tool.name}on ${on_string}: alignment (clustal)">
189 label="${tool.name}on ${on_string}: alignment (clustal)">
190 <filter>'clustal_strict' in outputs</filter> 160 <filter>'clustal_strict' in outputs</filter>
191 </data> 161 </data>
192 <data format="stockholm" name="stockholm" 162 <data format="stockholm" name="stockholm" label="${tool.name} on ${on_string}: alignment (stockholm)">
193 label="${tool.name} on ${on_string}: alignment (stockholm)">
194 <filter>'stockholm' in outputs</filter> 163 <filter>'stockholm' in outputs</filter>
195 </data> 164 </data>
196 <data format="txt" name="pp" 165 <data format="txt" name="pp" label="${tool.name} on ${on_string}: alignment (PP 2.0)">
197 label="${tool.name} on ${on_string}: alignment (PP 2.0)">
198 <filter>'pp' in outputs</filter> 166 <filter>'pp' in outputs</filter>
199 </data> 167 </data>
200 </outputs> 168 </outputs>
201 169
202 <tests> 170 <tests>