Mercurial > repos > rnateam > structure_to_gspan

comparison structure_to_gspan.xml @ 0:4c7736b4d8ff 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 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
author rnateam
date Mon, 22 May 2017 12:43:01 -0400
parents
children d62d7e98a68e
comparison
equal deleted inserted replaced
-1:000000000000 0:4c7736b4d8ff
1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.1">
2 <requirements>
3 <requirement type="package" version="0.2.0">graphclust-wrappers</requirement>
4 </requirements>
5 <command detect_errors="exit_code">
6 <![CDATA[
7 mkdir ./temp/ ./GSPAN_Outputs/ &&
8 structure_2_gspan.pl
9 --input-file '$dataFile'
10 --input-format 'rnafold'
11 $abstr
12 $stack
13 $seq_graph_t
14 -group $group
15 -tmp ./temp
16 -o ./GSPAN_Outputs/
17 ]]>
18 </command>
19 <inputs>
20 <param type="data" name="dataFile" format="dbn" label="Sequence and Structure input file in the prediction tool format" />
21 <param name="inputFormat" type="text" value="rnafold"
22 label=" Sequence Structure format of the input. Allowed format: rnafold" help="-input-format"/>
23 <param argument="-stack" truevalue="-stack" falsevalue="" checked="true" type="boolean"
24 label="Add stacking information to graphs"/>
25 <param argument="abstr" truevalue="-abstr" falsevalue="" type="boolean"
26 label="Add abstract structure graphs to the single shrep graph instances."/>
27 <param argument="-seq-graph-t" name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="true" type="boolean"
28 label="Add for each 't #' a graph which contains no structure"/>
29 <param name="group" type="integer" value="10000"
30 label="Group size" help="Default is 10000"/>
31 </inputs>
32 <outputs>
33 <collection name="gspan_compressed" type="list" label="GSPAN Groups" >
34 <discover_datasets pattern="(?P&lt;name&gt;.*)\.bz2$" directory="GSPAN_Outputs" />
35 </collection>
36 </outputs>
37 <tests>
38 <test>
39 <param name="dataFile" value="sample_3.struct"/>
40 <param name="i_stacks" value="True" />
41 <param name="i_abstr" value="False" />
42 <param name="seq_graph_t" value="True" />
43 <param name="group" value="10000" />
44 <output_collection name="gspan_compressed" type="list">
45 <element name="1.group.gspan" file="GSPAN_Outputs/sample_3.1.group.gspan.bz2"/>
46 </output_collection>
47 </test>
48 </tests>
49 <help>
50 <![CDATA[
51
52 **What it does**
53 For each pair of sequence and structure provided in the input file
54 and convert them into GSPAN format graphs.
55
56
57 **Parameters**
58
59 + **input** : The sequence and structure data, the output of structure prediction tool.
60
61 + **input-format** : Sequence Structure format of the input. Allowed format: "rnafold"
62 example of input-file for rnafold format:
63 >seq1
64 CCGGGCGUGCUG
65 .(((.....))) ( -0.30)
66 >seq2
67 GCGGUUGCCG
68 .(((...))) ( -0.50)
69
70
71 + **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.
73
74 + **abstr** : Add abstract structure graphs to the single shrep graph instances.
75
76 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
77
78 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
79
80 ]]>
81 </help>
82 <citations>
83 <citation type="doi">10.1093/bioinformatics/bts224</citation>
84 </citations>
85 </tool>