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comparison structure_to_gspan.xml @ 2:dcc336102d65 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 04:55:20 -0500
parents 133fc317a812
children d34ab3aa1724
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1:133fc317a812 2:dcc336102d65
1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.2"> 1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.3" >
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.3.1">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 which structure_2_gspan.pl &&
51 </test> 51 </test>
52 </tests> 52 </tests>
53 <help> 53 <help>
54 <![CDATA[ 54 <![CDATA[
55 55
56 **What it does** 56 **What it does**
57 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
58 and convert them into GSPAN format graphs. 58 and convert them into GSPAN format graphs.
59 59
60 60
61 **Parameters** 61 **Parameters**
62 62
63 + **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.
64 64
65 + **input-format** : Sequence Structure format of the input. Allowed format: "vrna-simple" "vrna-mea" 65 + **input-format** : Sequence Structure format of the input. Allowed format: "vrna-simple" "vrna-mea"
66 example of input-file for vrna-simple format: 66
67 >seq1 67 example of input-file for vrna-simple format:
68 CCGGGCGUGCUG 68 >seq1
69 .(((.....))) ( -0.30) 69 CCGGGCGUGCUG
70 >seq2 70 .(((.....))) ( -0.30)
71 GCGGUUGCCG 71 >seq2
72 .(((...))) ( -0.50) 72 GCGGUUGCCG
73 .(((...))) ( -0.50)
73 74
74 example of input-file for vrna-simple format: 75 example of input-file for vrna-simple format:
75 >seq1 76 >seq1
76 CCGGGCGUGCUG 77 CCGGGCGUGCUG
77 .(((.....))) ( -0.30) 78 .(((.....))) ( -0.30)
78 .{{{.....}}} [ -0.67] 79 .{{{.....}}} [ -0.67]
79 .(((.....))) { -0.30 d=1.29} 80 .(((.....))) { -0.30 d=1.29}
80 .(((.....))) { -0.30 MEA=9.52} 81 .(((.....))) { -0.30 MEA=9.52}
81 frequency of mfe structure in ensemble 0.550454; ensemble diversity 1.58 82 frequency of mfe structure in ensemble 0.550454; ensemble diversity 1.58
82 >seq2 83 >seq2
83 GCGGUUGCCG 84 GCGGUUGCCG
84 .(((...))) ( -0.50) 85 .(((...))) ( -0.50)
85 .({{...)}, [ -0.99] 86 .({{...)}, [ -0.99]
86 ..((...)). { 0.60 d=1.89} 87 ..((...)). { 0.60 d=1.89}
87 .(((...))) { -0.50 MEA=6.60} 88 .(((...))) { -0.50 MEA=6.60}
88 frequency of mfe structure in ensemble 0.452041; ensemble diversity 2.26 89 frequency of mfe structure in ensemble 0.452041; ensemble diversity 2.26
89 90
90 91
91 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges 92 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
92 (type p) from each of the involved bases to the new vertex. 93 (type p) from each of the involved bases to the new vertex.
93 94
94 + **abstr** : Add abstract structure graphs to the single shrep graph instances. 95 + **abstr** : Add abstract structure graphs to the single shrep graph instances.
95 96
96 + **seq-graph-t** : Add for each 't #' a graph which contains no structure 97 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
97 98
98 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2' 99 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
99 100
100 ]]> 101 ]]>
101 </help> 102 </help>
102 <citations> 103 <citations>
103 <citation type="doi">10.1093/bioinformatics/bts224</citation> 104 <citation type="doi">10.1093/bioinformatics/bts224</citation>