Mercurial > repos > rnateam > structure_to_gspan
changeset 1:133fc317a812 draft
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 |
| files | structure_to_gspan.xml |
| diffstat | 1 files changed, 27 insertions(+), 7 deletions(-) [+] |
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--- a/structure_to_gspan.xml Mon May 22 12:44:17 2017 -0400 +++ b/structure_to_gspan.xml Tue Jul 18 01:44:04 2017 -0400 @@ -1,13 +1,15 @@ -<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.1"> +<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.2"> <requirements> - <requirement type="package" version="0.2.0">graphclust-wrappers</requirement> + <requirement type="package" version="0.3.1">graphclust-wrappers</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ mkdir ./temp/ ./GSPAN_Outputs/ && + which structure_2_gspan.pl && structure_2_gspan.pl --input-file '$dataFile' - --input-format 'rnafold' + --input-format '$inputFormat' + --input-structure-type '$structureType' $abstr $stack $seq_graph_t @@ -18,8 +20,10 @@ </command> <inputs> <param type="data" name="dataFile" format="dbn" label="Sequence and Structure input file in the prediction tool format" /> - <param name="inputFormat" type="text" value="rnafold" - label=" Sequence Structure format of the input. Allowed format: rnafold" help="-input-format"/> + <param name="inputFormat" type="text" value="vrna-simple" + label=" Sequence Structure format of the input. Allowed formats: vrna-simple, vrna-mea" help="-input-format"/> + <param name="structureType" type="text" value="MFE" + label=" Sequence Structure type from the input to use. Allowed types: MFE, MEA" help="-input-structure-type"/> <param argument="-stack" truevalue="-stack" falsevalue="" checked="true" type="boolean" label="Add stacking information to graphs"/> <param argument="abstr" truevalue="-abstr" falsevalue="" type="boolean" @@ -58,8 +62,8 @@ + **input** : The sequence and structure data, the output of structure prediction tool. -+ **input-format** : Sequence Structure format of the input. Allowed format: "rnafold" - example of input-file for rnafold format: ++ **input-format** : Sequence Structure format of the input. Allowed format: "vrna-simple" "vrna-mea" + example of input-file for vrna-simple format: >seq1 CCGGGCGUGCUG .(((.....))) ( -0.30) @@ -67,6 +71,22 @@ GCGGUUGCCG .(((...))) ( -0.50) + example of input-file for vrna-simple format: + >seq1 + CCGGGCGUGCUG + .(((.....))) ( -0.30) + .{{{.....}}} [ -0.67] + .(((.....))) { -0.30 d=1.29} + .(((.....))) { -0.30 MEA=9.52} + frequency of mfe structure in ensemble 0.550454; ensemble diversity 1.58 + >seq2 + GCGGUUGCCG + .(((...))) ( -0.50) + .({{...)}, [ -0.99] + ..((...)). { 0.60 d=1.89} + .(((...))) { -0.50 MEA=6.60} + frequency of mfe structure in ensemble 0.452041; ensemble diversity 2.26 + + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges (type p) from each of the involved bases to the new vertex.