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comparison structure_to_gspan.xml @ 1:d62d7e98a68e draft

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planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author rnateam
date Mon, 20 Nov 2017 05:01:43 -0500
parents 4c7736b4d8ff
children 6648b5c2ce54
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0:4c7736b4d8ff 1:d62d7e98a68e
1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.1"> 1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.3" >
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.0">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.5.2">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"
47 </test> 51 </test>
48 </tests> 52 </tests>
49 <help> 53 <help>
50 <![CDATA[ 54 <![CDATA[
51 55
52 **What it does** 56 **What it does**
53 For each pair of sequence and structure provided in the input file 57 For each pair of sequence and structure provided in the input file
54 and convert them into GSPAN format graphs. 58 and convert them into GSPAN format graphs.
55 59
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
63 >seq1 67 example of input-file for vrna-simple format:
64 CCGGGCGUGCUG 68 >seq1
65 .(((.....))) ( -0.30) 69 CCGGGCGUGCUG
66 >seq2 70 .(((.....))) ( -0.30)
67 GCGGUUGCCG 71 >seq2
68 .(((...))) ( -0.50) 72 GCGGUUGCCG
73 .(((...))) ( -0.50)
69 74
70 75 example of input-file for vrna-simple format:
71 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges 76 >seq1
72 (type p) from each of the involved bases to the new vertex. 77 CCGGGCGUGCUG
78 .(((.....))) ( -0.30)
79 .{{{.....}}} [ -0.67]
80 .(((.....))) { -0.30 d=1.29}
81 .(((.....))) { -0.30 MEA=9.52}
82 frequency of mfe structure in ensemble 0.550454; ensemble diversity 1.58
83 >seq2
84 GCGGUUGCCG
85 .(((...))) ( -0.50)
86 .({{...)}, [ -0.99]
87 ..((...)). { 0.60 d=1.89}
88 .(((...))) { -0.50 MEA=6.60}
89 frequency of mfe structure in ensemble 0.452041; ensemble diversity 2.26
73 90
74 + **abstr** : Add abstract structure graphs to the single shrep graph instances. 91
92 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
93 (type p) from each of the involved bases to the new vertex.
75 94
76 + **seq-graph-t** : Add for each 't #' a graph which contains no structure 95 + **abstr** : Add abstract structure graphs to the single shrep graph instances.
77 96
78 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2' 97 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
98
99 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
79 100
80 ]]> 101 ]]>
81 </help> 102 </help>
82 <citations> 103 <citations>
83 <citation type="doi">10.1093/bioinformatics/bts224</citation> 104 <citation type="doi">10.1093/bioinformatics/bts224</citation>