Mercurial > repos > rnateam > graphclust_fasta_to_gspan

annotate fasta2shrep_gspan.xml @ 3:6942ec989fed draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 5a545fc913b3a07e1452e67f66b2ca593660abdf
author rnateam
date Mon, 27 Feb 2017 12:02:23 -0500
parents e79394322900
children aae41396646e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
1 <tool id="gspan" name="fasta_to_gspan" version="0.1">
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
2 <requirements>
3
6942ec989fed planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 5a545fc913b3a07e1452e67f66b2ca593660abdf
rnateam
parents: 2
diff changeset
3 <requirement type="package" version="0.1.9">graphclust-wrappers</requirement>
0
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
4 <requirement type="package" version="2.1.6">rnashapes</requirement>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
5 </requirements>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
6 <stdio>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
7 <exit_code range="1:" />
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
8 </stdio>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
9 <command>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
10 <![CDATA[
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
11
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
12 'fasta2shrep_gspan.pl' --fasta '$dataFasta' $i_crop_unpaired_ends $i_abstr $i_stacks -t "3=0,5=80" -M $M -c $rel_energy_range -win $wins -shift $shift $u $seq_graph_t --group $group
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
13
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
14 ]]>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
15 </command>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
16 <inputs>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
17 <param type="data" name="dataFasta" format="fasta" />
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
18 <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True" type="boolean" label="Add stacking information to graphs." help="-stack"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
19 <param name="i_abstr" truevalue="-abstr" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
20 <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
21 <param name="M" type="integer" value="5" size="7" label="Max number of shreps that should be taken per window." help="-M"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
22 <param name="rel_energy_range" type="integer" value="20" size="7" label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
23 <param name="wins" type="text" value="40,150" size="20" label=" A list of window sizes to use" help="comma separated integers"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
24 <param name="shift" type="integer" value="30" size="7" label="The shift of the window, relative to the window size given inpercent." help="by default 30"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
25 <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean" label="Ignore unstable structures (RNAshapes)" help="-u"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
26 <param name="seq_graph_t" truevalue="--seq-graph-t" falsevalue="" checked="True" type="boolean" label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
27 <param name="group" type="integer" value="10000" size="7" label="Group size." help="by default 10000"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
28 </inputs>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
29 <outputs>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
30 <data name="gspan.zip" format="searchgui_archive" from_work_dir="GSPAN_Outputs/1.group.gspan.bz2" label="gspan zip" />
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
31 </outputs>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
32 <tests>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
33 <test>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
34 <param name="dataFasta" value="data.fasta"/>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
35 <output name="gspan.zip" file="GSPAN_Outputs/1.group.gspan.bz2" />
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
36 </test>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
37 </tests>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
38 <help>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
39 <![CDATA[
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
40
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
41 **What it does**
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
42
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
43 For each fragment of input sequence we use RNAshapes to create a set of structures.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
44 The default parameters for example consider for each input fragment again a
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
45 window of size 40nt and 150nt with a window shift of 30%. This allows to
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
46 consider local structures as well as global structures for a fragment.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
47 From each such RNAshape window we take the top 5 shreps (suboptimal
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
48 structures for the top 5 shapes) within 20% of the mfe energy of that window
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
49 and convert them into graphs.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
50 As shape level (abstraction level) we use 3 for short sequences and 5 for
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
51 sequences >= 80nt. Please see also RNAshapes documentation for all these
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
52 terms.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
53
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
54
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
55 **Parameters**
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
56
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
57 + **input** : Sequences in Fasta format.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
58
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
59 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
60 (type p) from each of the involved bases to the new vertex.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
61
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
62 + **abstr** : Add abstract structure graphs to the single shrep graph instances.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
63
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
64 + **cue** : Crop unpaired ends. If you give this flag, then the unpaired ends of each single structure are ignored. E.g. the structure
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
65 ...(((...))).. becomes just (((...)))
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
66
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
67 + **M** : Max number of shreps that should be taken per window.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
68
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
69 + **c** : Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes) Use only one of -e and -c!
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
70
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
71 + **wins** : A list of window sizes to use. If none are given (empty string ''), then the entire sequence is taken with no windows. Each window > 1 required!
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
72
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
73 + **shift** : The shift of the window, relative to the window size given in percent. So you give which percent of the window size shall be
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
74 used for the shift. Of course the shift is rounded down to the
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
75 nearest whole number.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
76 Example 20 % of a window 150 would result in a step size of 30 nt.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
77 It is a relative parameter, as you can give different window sizes.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
78 If you do not give this parameter there is a default shift of 1 nt.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
79
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
80 + **u** : Ignore unstable structures (RNAshapes). This option filters out closed structures with positive free energy.
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
81
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
82 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
83
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
84 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
85
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
86 ]]>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
87 </help>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
88 <citations>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
89 <citation type="doi">10.1093/bioinformatics/bts224</citation>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
90 <citation type="bibtex">@article{jan:gie:2015,
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
91 author={Janssen, Stefan and Giegerich, Robert},
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
92 title={The RNA shapes studio},
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
93 journal={Bioinformatics},
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
94 year={2015},
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
95 doi={10.1093/bioinformatics/btu649},
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
96 url={http://bioinformatics.oxfordjournals.org/content/31/3/423.abstract}}</citation>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
97 </citations>
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
98 </tool>