Mercurial > repos > rnateam > structure_to_gspan

annotate structure_to_gspan.xml @ 0:4c7736b4d8ff draft

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