Mercurial > repos > rnateam > structure_to_gspan

annotate structure_to_gspan.xml @ 1:d62d7e98a68e 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 05:01:43 -0500
parents 4c7736b4d8ff
children 6648b5c2ce54
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d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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1 <tool id="structure_to_gspan" name="Structure to GSPAN" version="0.3" >
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2 <requirements>
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3 <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code">
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6 <![CDATA[
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7 mkdir ./temp/ ./GSPAN_Outputs/ &&
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d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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8 which structure_2_gspan.pl &&
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9 structure_2_gspan.pl
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10 --input-file '$dataFile'
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d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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11 --input-format '$inputFormat'
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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12 --input-structure-type '$structureType'
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13 $abstr
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14 $stack
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15 $seq_graph_t
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16 -group $group
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17 -tmp ./temp
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18 -o ./GSPAN_Outputs/
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param type="data" name="dataFile" format="dbn" label="Sequence and Structure input file in the prediction tool format" />
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23 <param name="inputFormat" type="text" value="vrna-simple"
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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24 label=" Sequence Structure format of the input. Allowed formats: vrna-simple, vrna-mea" help="-input-format"/>
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25 <param name="structureType" type="text" value="MFE"
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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26 label=" Sequence Structure type from the input to use. Allowed types: MFE, MEA" help="-input-structure-type"/>
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27 <param argument="-stack" truevalue="-stack" falsevalue="" checked="true" type="boolean"
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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28 label="Add stacking information to graphs"/>
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29 <param argument="abstr" truevalue="-abstr" falsevalue="" type="boolean"
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30 label="Add abstract structure graphs to the single shrep graph instances."/>
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31 <param argument="-seq-graph-t" name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="true" type="boolean"
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32 label="Add for each 't #' a graph which contains no structure"/>
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33 <param name="group" type="integer" value="10000"
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34 label="Group size" help="Default is 10000"/>
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35 </inputs>
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36 <outputs>
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37 <collection name="gspan_compressed" type="list" label="GSPAN Groups" >
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38 <discover_datasets pattern="(?P&lt;name&gt;.*)\.bz2$" directory="GSPAN_Outputs" />
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39 </collection>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="dataFile" value="sample_3.struct"/>
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44 <param name="i_stacks" value="True" />
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45 <param name="i_abstr" value="False" />
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46 <param name="seq_graph_t" value="True" />
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47 <param name="group" value="10000" />
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48 <output_collection name="gspan_compressed" type="list">
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49 <element name="1.group.gspan" file="GSPAN_Outputs/sample_3.1.group.gspan.bz2"/>
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50 </output_collection>
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51 </test>
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52 </tests>
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53 <help>
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54 <![CDATA[
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55
1
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56 **What it does**
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57 For each pair of sequence and structure provided in the input file
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58 and convert them into GSPAN format graphs.
0
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59
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60
1
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61 **Parameters**
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62
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63 + **input** : The sequence and structure data, the output of structure prediction tool.
0
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64
1
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65 + **input-format** : Sequence Structure format of the input. Allowed format: "vrna-simple" "vrna-mea"
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66
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67 example of input-file for vrna-simple format:
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68 >seq1
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69 CCGGGCGUGCUG
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70 .(((.....))) ( -0.30)
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71 >seq2
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72 GCGGUUGCCG
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73 .(((...))) ( -0.50)
0
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74
1
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75 example of input-file for vrna-simple format:
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76 >seq1
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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77 CCGGGCGUGCUG
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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78 .(((.....))) ( -0.30)
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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79 .{{{.....}}} [ -0.67]
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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80 .(((.....))) { -0.30 d=1.29}
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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81 .(((.....))) { -0.30 MEA=9.52}
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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82 frequency of mfe structure in ensemble 0.550454; ensemble diversity 1.58
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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83 >seq2
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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84 GCGGUUGCCG
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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85 .(((...))) ( -0.50)
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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86 .({{...)}, [ -0.99]
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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87 ..((...)). { 0.60 d=1.89}
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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88 .(((...))) { -0.50 MEA=6.60}
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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89 frequency of mfe structure in ensemble 0.452041; ensemble diversity 2.26
0
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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90
1
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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91
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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92 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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93 (type p) from each of the involved bases to the new vertex.
0
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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94
1
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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95 + **abstr** : Add abstract structure graphs to the single shrep graph instances.
0
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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96
1
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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97 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
0
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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98
1
d62d7e98a68e planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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99 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
0
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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100
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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101 ]]>
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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102 </help>
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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103 <citations>
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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104 <citation type="doi">10.1093/bioinformatics/bts224</citation>
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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105 </citations>
4c7736b4d8ff planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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106 </tool>