Mercurial > repos > rnateam > structure_to_gspan
changeset 2:dcc336102d65 draft
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 |
| files | structure_to_gspan.xml |
| diffstat | 1 files changed, 37 insertions(+), 36 deletions(-) [+] |
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--- a/structure_to_gspan.xml Tue Jul 18 01:44:04 2017 -0400 +++ b/structure_to_gspan.xml Mon Nov 20 04:55:20 2017 -0500 @@ -1,6 +1,6 @@ -<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.2"> +<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.3" > <requirements> - <requirement type="package" version="0.3.1">graphclust-wrappers</requirement> + <requirement type="package" version="0.5.2">graphclust-wrappers</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -53,49 +53,50 @@ <help> <![CDATA[ -**What it does** -For each pair of sequence and structure provided in the input file -and convert them into GSPAN format graphs. + **What it does** + For each pair of sequence and structure provided in the input file + and convert them into GSPAN format graphs. -**Parameters** + **Parameters** -+ **input** : The sequence and structure data, the output of structure prediction tool. + + **input** : The sequence and structure data, the output of structure prediction tool. -+ **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) - >seq2 - GCGGUUGCCG - .(((...))) ( -0.50) + + **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) + >seq2 + 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 + 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. + + + **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. -+ **abstr** : Add abstract structure graphs to the single shrep graph instances. + + **abstr** : Add abstract structure graphs to the single shrep graph instances. -+ **seq-graph-t** : Add for each 't #' a graph which contains no structure + + **seq-graph-t** : Add for each 't #' a graph which contains no structure -+ **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2' + + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2' ]]> </help>