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comparison locarna_pairwise.xml @ 1:b06dc2bb3716 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 16:49:33 -0500
parents 6a79a086fa50
children 433601e9f132
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0:6a79a086fa50 1:b06dc2bb3716
1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.0"> 1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.1">
2 <description> 2 <description>
3 Pairwise Simultaneous Alignment and Folding of RNAs 3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna" 38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
39 --sequ-local on 39 --sequ-local on
40 --struct-local on 40 --struct-local on
41 #end if 41 #end if
42 42
43 ## -------------------- scoring parameters 43 @SCORING_ARGS@
44 44
45 --indel $Scoring.indel 45 @FOLDING_ARGS@
46 --indel-opening $Scoring.indel_opening
47 --struct-weight $Scoring.struct_weight
48 --tau $Scoring.tau
49
50 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
51 --match $Scoring.sequence_score.match
52 --mismatch $Scoring.sequence_score.mismatch
53 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
54 --use-ribosum true
55 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
56 --ribofit true
57 #end if
58
59 ## -------------------- folding parameters
60
61 #if float($Folding.rnafold_temperature) != 37.0
62 --rnafold-temperature $Folding.rnafold_temperature
63 #end if
64
65 $Folding.alifold_consensus_dp 46 $Folding.alifold_consensus_dp
66 --consensus-structure $Folding.consensus_structure 47 --consensus-structure $Folding.consensus_structure
67 48
68 ## -------------------- heuristic parameters 49 @HEURISTIC_ARGS@
69 50
70 -p $Heuristics.min_prob 51 @CONSTRAINT_ARGS@
71 --max-diff-am $Heuristics.max_diff_am 52
72 --max-diff $Heuristics.max_diff
73 --max-diff-at-am $Heuristics.max_diff_at_am
74
75 #if float($Heuristics.max_bps_length_ratio) != 0.0
76 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
77 #end if
78
79 ## -------------------- other parameters
80
81 $Constraint.lonely_pairs
82
83 #if $Constraint.maxBPspan != -1
84 --maxBPspan $Constraint.maxBPspan
85 #end if
86
87 $Constraint.ignore_constraints
88
89 ## -------------------- output 53 ## -------------------- output
90 54
91 #if 'stockholm' in str($outputs).split(",") 55 #if 'stockholm' in str($outputs).split(",")
92 --stockholm '$stockholm' 56 --stockholm '$stockholm'
93 #end if 57 #end if
99 #end if 63 #end if
100 #if 'pp' in str($outputs).split(",") 64 #if 'pp' in str($outputs).split(",")
101 --pp '$pp' 65 --pp '$pp'
102 #end if 66 #end if
103 67
104 $stdout_verbosity 68 @STDOUT_ARGS@
105
106 #if str($stdout_verbosity) != "--quiet":
107 > '$stdout'
108 #end if
109 69
110 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",") 70 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
111 && cp $clustal $clustal_strict 71 && cp $clustal $clustal_strict
112 #end if 72 #end if
113 73
114 #if 'clustal_strict' in str($outputs).split(",") 74 #if 'clustal_strict' in str($outputs).split(",")
115 && sed -i '/\^#/d' '$clustal_strict' 75 && cp '$clustal_strict' '$clustal_strict~'
76 && sed '/^#/d' '$clustal_strict~' >'$clustal_strict'
116 #end if 77 #end if
117 78
118 ]]></command> 79 ]]></command>
119 80
120 <inputs> 81 <inputs>
198 </param> 159 </param>
199 </section> 160 </section>
200 161
201 <section name="Heuristics" title="Heuristic parameters"> 162 <section name="Heuristics" title="Heuristic parameters">
202 <expand macro="common_heuristic_parameters" /> 163 <expand macro="common_heuristic_parameters" />
203 </section> 164 <expand macro="max_diff_parameters_aln" />
204 165 </section>
205 <section name="Constraint" title="Constraint parameters"> 166
206 <expand macro="constraints" /> 167 <section name="Constraints" title="Constraint parameters">
168 <expand macro="common_constraint_parameters" />
207 </section> 169 </section>
208 </inputs> 170 </inputs>
209 171
210 <outputs> 172 <outputs>
211 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> 173 <expand macro="standard_outupt" />
212 <filter>stdout_verbosity != '--quiet'</filter>
213 </data>
214 <data format="clustal" name="clustal" 174 <data format="clustal" name="clustal"
215 label="${tool.name} alignment (annotated clustal) on ${on_string}"> 175 label="${tool.name} alignment (annotated clustal) on ${on_string}">
216 <filter>'clustal' in outputs</filter> 176 <filter>'clustal' in outputs</filter>
217 </data> 177 </data>
218 <data format="clustal" name="clustal_strict" 178 <data format="clustal" name="clustal_strict"
232 <tests> 192 <tests>
233 <test> 193 <test>
234 <param name="inputA" value="tRNA_2-1.fa" /> 194 <param name="inputA" value="tRNA_2-1.fa" />
235 <param name="inputB" value="tRNA_2-2.fa" /> 195 <param name="inputB" value="tRNA_2-2.fa" />
236 <param name="outputs" value="clustal" /> 196 <param name="outputs" value="clustal" />
237 <output name="clustal" file="tRNA_2.aln" /> 197 <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
198 </test>
199 <test>
200 <param name="inputA" value="haca.snoRNA-1.aln" />
201 <param name="inputB" value="haca.snoRNA-2.aln" />
202 <param name="outputs" value="clustal_strict,clustal" />
203 <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" />
204 <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="1" />
238 </test> 205 </test>
239 </tests> 206 </tests>
240 207
241 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs** 208 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
242 209