Mercurial > repos > rnateam > structure_to_gspan

comparison structure_to_gspan.xml @ 1:133fc317a812 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 746497a64b955f6b9afc1944d1c1d8d877e53267
author rnateam
date Tue, 18 Jul 2017 01:44:04 -0400
parents e47ad1f7411a
children dcc336102d65
comparison
equal deleted inserted replaced
0:e47ad1f7411a 1:133fc317a812
1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.1"> 1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.0">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.3.1">graphclust-wrappers</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"> 5 <command detect_errors="exit_code">
6 <![CDATA[ 6 <![CDATA[
7 mkdir ./temp/ ./GSPAN_Outputs/ && 7 mkdir ./temp/ ./GSPAN_Outputs/ &&
8 which structure_2_gspan.pl &&
8 structure_2_gspan.pl 9 structure_2_gspan.pl
9 --input-file '$dataFile' 10 --input-file '$dataFile'
10 --input-format 'rnafold' 11 --input-format '$inputFormat'
12 --input-structure-type '$structureType'
11 $abstr 13 $abstr
12 $stack 14 $stack
13 $seq_graph_t 15 $seq_graph_t
14 -group $group 16 -group $group
15 -tmp ./temp 17 -tmp ./temp
16 -o ./GSPAN_Outputs/ 18 -o ./GSPAN_Outputs/
17 ]]> 19 ]]>
18 </command> 20 </command>
19 <inputs> 21 <inputs>
20 <param type="data" name="dataFile" format="dbn" label="Sequence and Structure input file in the prediction tool format" /> 22 <param type="data" name="dataFile" format="dbn" label="Sequence and Structure input file in the prediction tool format" />
21 <param name="inputFormat" type="text" value="rnafold" 23 <param name="inputFormat" type="text" value="vrna-simple"
22 label=" Sequence Structure format of the input. Allowed format: rnafold" help="-input-format"/> 24 label=" Sequence Structure format of the input. Allowed formats: vrna-simple, vrna-mea" help="-input-format"/>
25 <param name="structureType" type="text" value="MFE"
26 label=" Sequence Structure type from the input to use. Allowed types: MFE, MEA" help="-input-structure-type"/>
23 <param argument="-stack" truevalue="-stack" falsevalue="" checked="true" type="boolean" 27 <param argument="-stack" truevalue="-stack" falsevalue="" checked="true" type="boolean"
24 label="Add stacking information to graphs"/> 28 label="Add stacking information to graphs"/>
25 <param argument="abstr" truevalue="-abstr" falsevalue="" type="boolean" 29 <param argument="abstr" truevalue="-abstr" falsevalue="" type="boolean"
26 label="Add abstract structure graphs to the single shrep graph instances."/> 30 label="Add abstract structure graphs to the single shrep graph instances."/>
27 <param argument="-seq-graph-t" name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="true" type="boolean" 31 <param argument="-seq-graph-t" name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="true" type="boolean"
56 60
57 **Parameters** 61 **Parameters**
58 62
59 + **input** : The sequence and structure data, the output of structure prediction tool. 63 + **input** : The sequence and structure data, the output of structure prediction tool.
60 64
61 + **input-format** : Sequence Structure format of the input. Allowed format: "rnafold" 65 + **input-format** : Sequence Structure format of the input. Allowed format: "vrna-simple" "vrna-mea"
62 example of input-file for rnafold format: 66 example of input-file for vrna-simple format:
63 >seq1 67 >seq1
64 CCGGGCGUGCUG 68 CCGGGCGUGCUG
65 .(((.....))) ( -0.30) 69 .(((.....))) ( -0.30)
66 >seq2 70 >seq2
67 GCGGUUGCCG 71 GCGGUUGCCG
68 .(((...))) ( -0.50) 72 .(((...))) ( -0.50)
73
74 example of input-file for vrna-simple format:
75 >seq1
76 CCGGGCGUGCUG
77 .(((.....))) ( -0.30)
78 .{{{.....}}} [ -0.67]
79 .(((.....))) { -0.30 d=1.29}
80 .(((.....))) { -0.30 MEA=9.52}
81 frequency of mfe structure in ensemble 0.550454; ensemble diversity 1.58
82 >seq2
83 GCGGUUGCCG
84 .(((...))) ( -0.50)
85 .({{...)}, [ -0.99]
86 ..((...)). { 0.60 d=1.89}
87 .(((...))) { -0.50 MEA=6.60}
88 frequency of mfe structure in ensemble 0.452041; ensemble diversity 2.26
69 89
70 90
71 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges 91 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
72 (type p) from each of the involved bases to the new vertex. 92 (type p) from each of the involved bases to the new vertex.
73 93